A review on cover crops as a multifunctional ecological regulator in organic crop production systems

1 Introduction

Organic agriculture has expanded globally as producers, consumers, and policy makers seek production systems which reduces dependence on synthetic inputs while maintaining soil health, ecosystem and human health. The global movement towards sustainable food systems has elevated the demand for organic agriculture as an alternative to input-intensive conventional production (Das et al., 2022). Organic agriculture is commonly framed as a biological production system that relies on ecological processes, biodiversity, and locally adapted biological cycles rather than synthetic inputs with adverse effects (FAO, 1999; IFOAM, 2008; Das et al., 2022). The proven ecological benefits of organic production include less agrochemical pollution, biodiversity conservation, and reduced synthetic resource usage. However, its widespread adoption and yield consistency are hampered by the reliance on slow-release, biologically mediated nutrient cycling systems that release nitrogen asynchronously relative to peak crop demand, leading to transient nutrient deficits that restrict productivity (Carr et al., 2012; Osterholz et al., 2021). Weed management also presents a formidable challenge; the ban on synthetic herbicides in certified organic systems requires reliance on mechanical and cultural practices that are labor-intensive, often unreliable, and ecologically disruptive if applied too frequently (Osterholz et al., 2021). These two constraints (nutrient asynchrony and weed pressure) are among the major contributors to the reduced productivity of organic systems relative to conventional systems (Quintarelli et al., 2022; Koudahe et al., 2022). In addressing these challenges, organic producers should include cover crops as a central technology in their management, which are among the most functionally diverse and ecologically sound management options available.

In this review, cover crops are defined as non-harvested or secondary annual or perennial plant species grown before, after, or between cash crops to provide agronomic and ecological services rather than direct marketable yield. We distinguish the cover crops into four categories based on related but not identical practices. First, cover crops retained on the soil surface after termination function primarily as dead mulch and are commonly associated with reduced or minimum tillage. Second, green manures are cover crops incorporated into the soil by tillage to accelerate residue decomposition and nutrient release. Third, living mulches are cover crops maintained during part or all of the cash crop season and therefore provide continuous soil cover but may compete with the crop for water, light, and nutrients. Fourth, cover crop-based reduced- or no-tillage systems combine cover crop biomass with low-disturbance termination methods such as roller-crimping, mowing, undercutting, strip tillage, or flaming (Table 1). This distinction is central because yield, weed, nutrient, and soil carbon responses may reflect not only the cover crop species but also whether residues are incorporated, retained on the surface, or maintained as a living stand (Casagrande et al., 2016; Vincent-Caboud et al., 2017; Adetunji et al., 2020; Koudahe et al., 2022; Scarlato et al., 2024). As shown in Table 1, the placement of residue and the level of soil disturbance strongly influence nutrient-release patterns, soil protection, weed suppression, and possible risks such as nitrogen immobilization, crop competition, or planting difficulty.

Table 1. Conceptual distinction among cover crop management pathways in organic crop production systems.

Legumes cover crops are emphasized as annual or short-season fertility-building species, whereas perennial legume species are discussed only when they are managed as living mulch, orchard floor vegetation, or short-term green manure crops. Small-grain cereals/grasses, brassicas and selected forbs cover crops are important for nitrate scavenging, erosion control, rapid soil cover, pollinator support and weed suppression depending on the climate and planting window (Adetunji et al., 2020; Koudahe et al., 2022). Cover crops enhance soil physical quality through root development and protective surface residues. Their roots support aggregation, biopore formation, and soil biological activity, while residues remaining on the soil surface help limit raindrop impact, runoff, erosion, crusting, and compaction. These benefits are particularly important in frequently tilled vegetable systems, where limited soil cover can increase degradation risk. However, increases in soil carbon are context-dependent and vary with initial SOC levels, existing soil conditions, biomass inputs, residue management, climate, and tillage intensity (García de Souza et al., 2011; Alliaume et al., 2013, 2014). Taken together, cover crops provide a range of ecosystem services, including accumulation of soil organic carbon, improvement of soil physical structure, stimulation of soil microbiome activity, weed suppression, and reduction of nutrient leaching losses (Yousefi et al., 2024; Salisu et al., 2025).

Cover crops have a significant impact on the physical, chemical, and biological properties of soil health, the core resource for creating efficient, productive organic systems. Cover crops are considered a key management tool for improving physical soil properties. Multiple cover cropping cycles increase soil aggregate stability, decrease bulk density, and increase water infiltration and retention, especially when biomass inputs are utilized effectively over several seasons (Blanco-Canqui and Ruis, 2020; Haruna et al., 2020). Non-leguminous species (grasses/cereals, brassicas and selected broad leaf forbs) are especially good at scavenging residual nitrate and phosphorus from the soil profile and preventing leaching losses during fallow periods (Adetunji et al., 2020; Scavo et al., 2022; Carr et al., 2013). Perhaps most functionally relevant to organic systems, cover crops reliably stimulate microbial biomass, shift microbial community composition toward more functionally diverse assemblages, and increase the activity of enzymes associated with nitrogen mineralization, phosphorus solubilization, and carbon cycling (Kim et al., 2020; Muhammad et al., 2021). While average effects on soil organic carbon stocks are positive, recent analyses suggest that gains are slower and more variable than sometimes reported. These gains depends strongly on the initial SOC level, the quantity and quality of above- and below-ground biomass inputs, as well as the stability of the carbon fractions formed (Moukanni et al., 2022; Chaplot and Smith, 2023; Salisu et al., 2025).

Weed management is another strategically important but context-dependent function of cover crops in organic systems. Cover crops can suppress weeds through living competition, surface mulch, allelopathic residue effects, and longer-term changes in weed seedbank density and species composition (Hartwig and Ammon, 2002; Mirsky et al., 2012; Baraibar et al., 2018a, 2018b; Osipitan et al., 2018; Navarro-Miró et al., 2019; Nichols et al., 2020; Bruce et al., 2022b; Fernando and Shrestha, 2023). These mechanisms make weed suppression a biological soil function rather than a service separate from soil biology. High-biomass cereals such as rye often provide strong physical suppression after termination, whereas legumes may provide nitrogen but weaker mulch persistence (Mirsky et al., 2012; Vollmer et al., 2010; Couëdel et al., 2018; Vogeler et al., 2022). Brassicas and other broadleaf species can contribute rapid canopy closure or bioactive residues, while species such as sunflower, buckwheat, and phacelia may be useful in specific rotations where rapid growth, pollinator support, or weed competition are priorities (Vollmer et al., 2010; Ciaccia et al., 2015; Quintarelli et al., 2022; Lalewicz et al., 2024). Nevertheless, cover crops rarely provide season-long weed control alone; their effectiveness depends on biomass, timing, weed community composition, seedbank history, and integration with cultivation, rotation, mulching, or other organic weed management tactics (Osipitan et al., 2018; Nichols et al., 2020; Fernando and Shrestha, 2023). The same traits that make cover crops useful can also create trade-offs. Low-C:N legume green manures may release nitrogen rapidly but may leave little surface mulch for weed suppression. High-C:N cereal residues provide persistent mulch and erosion protection but can immobilize nitrogen, delay soil warming, or interfere with planting. Living mulches can maintain continuous roots and suppress weeds but may compete with shallow-rooted vegetables or young perennial crops. Reduced-tillage cover crop systems can improve surface soil protection and biological activity, but organic systems lack herbicide back-up; incomplete termination, perennial weed escapes, and insufficient nitrogen availability can reduce cash crop yield (Carr et al., 2012; Mirsky et al., 2012; Hefner et al., 2020; Scarlato et al., 2024). Therefore, this review adopts a systems-based framework in which cover crops are considered multifunctional ecological regulators whose benefits are conditional rather than automatic. The success of cover cropping depends on the interaction among cover crop species or mixtures, planting and termination timing, biomass quantity and quality, residue management, subsequent cash crop management, and site-specific soil and environmental conditions. Thus, cover cropping is best understood as a system-thinking technology, where outcomes emerge from the coordination of cover crop choice, management practices, and broader agroecosystem context rather than from the mere presence or absence of a cover crop.

Despite the increasing amount of research on cover crops in organic and conventional systems, several critical knowledge gaps remain. Research conducted under certified organic management systems is underrepresented relative to the overall volume of published research, and the transferability of findings from conventionally managed systems (where soil fertility baselines, pest complexes, and management histories can be very different) cannot be assumed (Osterholz et al., 2021; Das et al., 2022). While there is evidence that cover crop management can be beneficial for organic production, it is disproportionately found in annual vegetable systems and temperate field crops, with relatively little data available for organic orchards, vineyards, herb production, and ornamental nurseries (Schoolman and Arbuckle, 2022). Cover crop management in combination with reduced or conservation tillage is an increasingly important practice for organic producers who want to reduce soil disturbance, yet it has been particularly understudied (Osterholz et al., 2021). Finally, there is very little long-term (over five years) experimental data, making it difficult to understand how cover crop-driven changes in soil biological communities and carbon fractions translate into sustainable increases in crop productivity (Koudahe et al., 2022; Scavo et al., 2022).

Against this background, our review provides mechanistic and management-oriented synthesis of cover crops in organic crop production systems. The central argument is that cover crops function as multifunctional ecological regulators only when their functional traits, termination strategy, residue placement, and crop-system context are aligned. This framing allows the review to integrate strengths, limitations, and knowledge gaps while avoiding the assumption that all cover crop uses are equivalent.

2 Overview of organic production systems

2.1 Adoption and economic significance

Organic agriculture has evolved from a small niche production system into one of the most rapidly growing segments of the global food economy. The FAO/Codex framework describes organic agriculture as a holistic production management system that promotes agroecosystem health, including biodiversity, biological cycles, and soil biological activity (FAO, 1999). IFOAM similarly defines organic agriculture as a production system that sustains the health of soils, ecosystems, and people by relying on ecological processes, biodiversity, and cycles adapted to local conditions (IFOAM, 2008). These definitions are directly relevant to cover crops because they position soil cover, living roots, biodiversity, and nutrient cycling as foundational components of organic system design rather than optional practices.

Recent global statistics further support the need to frame organic agriculture from an international perspective. According to the FiBL and IFOAM report The World of Organic Agriculture 2026, organic agriculture is now practiced in more than 180 countries, with nearly 99 million hectares of agricultural land managed organically by at least 4.8 million farmers. Global sales of organic food and drink reached almost €145 billion, demonstrating that organic agriculture has become a major component of the global food economy rather than a niche sector (Willer et al., 2026). Europe represents one of the most developed organic regions, with organic retail sales reaching €58.7 billion in 2024, including €49.5 billion within the European Union. Germany remained the largest organic market in Europe, while Switzerland recorded the highest per capita organic consumption and the highest organic market share worldwide (FiBL, 2026). At the same time, the European Union had approximately 10.8% of its agricultural land under organic management in 2023, indicating substantial progress but also showing that further expansion is needed to reach the EU Farm to Fork target of 25% organic agricultural land by 2030 (European Environment Agency, 2025).

U.S. statistics are retained below as one regional market example, two complementary data sources track the economic scale and momentum of this growth in the United States: the USDA National Agricultural Statistics Service (NASS) Organic Survey program, which monitors certified farm-level production and sales, and the Organic Trade Association (OTA) annual Organic Market Report, which compiles retail-level consumer sales across all organic product categories. According to the OTA, 2026 Organic Market Report, which included survey and interview data collected from November 2025 through January 2026, U.S. certified organic sales in 2025 were $76.6 billion, representing an annual growth rate of 6.8%, compared to 3.4% for the broader conventional marketplace. Organic food sales in 2025 were $70.1 billion, or 6.1% of the total food market – with a growth rate outpacing that of the total food market for the third straight year. Fresh produce was the top organic category – and remained the primary gateway for new organic consumers – with sales of $22.7 billion (30% of all organic sales) and a 5.3% growth rate (OTA, 2026). The OTA projects a 5.6% compound annual growth rate for organics and predicts total sales will exceed $100 billion by 2030.

In 2022, the USDA Census of Agriculture recorded sales of $9.6 billion for certified or exempt organic products, up 32% from the 2017 census, even as the number of farms reporting organic sales fell 5% to 17,321. Organic production was geographically concentrated, with California accounting for 39% of all sales ($3.7 billion), which was more than four times that of Washington, the next-highest state, followed by Pennsylvania, Texas, and Oregon. Nine of the top ten organic-producing counties were in California, led by Monterey County, whose $740 million in organic sales represented approximately 8% of all such sales nationwide. In terms of commodity type, vegetables and melons ($2.3 billion); fruits, tree nuts, and berries ($2.2 billion); and poultry and eggs ($2 billion) made up 67% of total organic sales (U.S. Department of Agriculture National Agricultural Statistics Service, 2024).

2.2 Principles of organic agriculture and soil-centered management

Organic agriculture is guided by the IFOAM principles of health, ecology, fairness, and care and it emphasize biodiversity, biological cycles, and soil biological activity (FAO, 1999; IFOAM, 2008). Within this framework the soil fertility must be built, and sustained through the crop rotations, organic matter management, cover cropping, composting and biological nutrient cycling, pest and weed regulation must rely primarily on cultural, mechanical, and biological approaches rather than synthetic chemical inputs (Das et al., 2017; Silva and Moore, 2017; Wittwer et al., 2017). These are not simply regulatory constraints but embodiments of a systems philosophy in which the health of the soil biological community is the key determinant of long-term crop productivity and farm resilience.

A survey of certified organic vegetable farms in Wisconsin (Silva and Moore, 2017) reported that cover crops, mainly cool-season legumes such as hairy vetch (Vicia villosa) and clovers, and small-grain cereals such as oats (Avena sativa) and winter rye (Secale cereale), were valued more for fertility, structure, and ecological function than for weed management. This extended Moore et al. (2016) findings that adoption intensity varied widely and was influenced more by management experience and farm-specific constraints than by awareness of cover crop benefits. These results confirm that technical knowledge and practical farm management capacity must advance in parallel to increase the effective use of cover crops in certified organic systems.

2.3 Soil fertility and weed management constraints

The fundamental agronomic challenge in organic systems is the mismatch between crop demand and the biological supply of nutrients from soil organic matter, cover crops, and compost residues. Soil temperature, moisture, substrate composition, and microbial community composition rarely align with the timing of peak nitrogen demand in transplanted or direct-seeded vegetable crops during establishment and rapid canopy expansion (Das et al., 2022). This asynchrony is most critical for nitrogen, which controls vegetative growth and marketable yield, but also applies to phosphorus, sulfur, and micronutrients, which depend on biological transformation pathways absent in inorganic fertilizer inputs. Therefore, organic producers must manage the soil biological system holistically, using combinations of cover crops, compost, tillage timing, and rotation design to optimize the rates of mineralization of nutrients stored in soil organic matter and in cover crop and compost residues (Norris and Congreves, 2018; Das et al., 2022).

Weed management in certified organic systems is equally challenging, as synthetic herbicides are prohibited. Mechanical cultivation, flame weeding, and cultural practices, such as tillage timing, diversified crop rotations, and the use of competitive cover crops, are more labor-intensive and less consistent in their effectiveness than herbicide application (Osterholz et al., 2021). Mechanical tillage is effective for weed control, but its repeated use destroys soil physical structure, decreases soil carbon, and runs counter to the organic production philosophy of building biological soil health (Osterholz et al., 2021). This tension between the need for mechanical weed management and the desire to minimize soil disturbance to improve biological health has led to a significant interest in cover crops as a biological weed management tool to reduce tillage frequency and intensity while still maintaining weed control (Fernando and Shrestha, 2023). Keeping the constraints of organic farming in context, the role of the cover crops in the organic production systems is discussed in the next sections.

3 Role of cover crops in organic agriculture

3.1 Functional classification

Legumes, grasses/cereals, brassicas, and selected broadleaf forbs, and mixtures of these constitute the main principal functional groups of cover crops (Table 2). While they vary in nitrogen economy, rooting architecture, biomass production potential, and residue chemistry, phenology and termination response each functional group provides a characteristic portfolio of agronomic services (Quintarelli et al., 2022; Scavo et al., 2022). Annual legumes, such as hairy vetch (Vicia villosa), common vetch (Vicia sativa), faba bean (Vicia faba), subterranean clover (Trifolium subterraneum), berseem clover (Trifolium alexandrinum), and crimson clover (Trifolium incarnatum) are most relevant where the short season nitrogen fixation or green manure effects are desired. Perennial legumes such as alfalfa (Medicago sativa), and white clover (Trifolium repens) are applied as a living mulch, orchard floor cover or short-term incorporated biomass because their management differs from annual dead mulch cover crops (Coombs et al., 2017; Basinger and Hill, 2021; Hill et al., 2021). Grasses and cereals, such as winter rye (Secale cereale), oats (Avena sativa), black oat (Avena strigosa), barley (Hordeum vulgare), and sorghum-sudan (Sorghum bicolor var. sudanese) hybrids, yield high above-ground biomass, develop fibrous root systems, and produce high C:N residues that can promote surface cover and weed suppression (Koudahe et al., 2022). Brassicas like fodder radish (Raphanus sativus var. longipinnatus), white mustard (Sinapis alba), and oilseed radish (Raphanus sativus var. oleifera) produce early ground cover, taproot biopores, and allelopathic compounds derived from glucosinolates, which are efficient in repelling soil nematode pests (Quintarelli et al., 2022). Broadleaf forbs such as sunflower (Helianthus annuus), phacelia (Phacelia tanacetifolia), and buckwheat (Fagopyrum esculentum) are also relevant because they can provide rapid canopy closure, pollinator resources, contrasting root traits, and weed-suppressive biomass depending on climate and planting window (Dillard, 2023; Lalewicz et al., 2024; Richwine et al., 2024). The summarization of these functional differences are mentioned in Table 2, and it highlights why species selection should be based on the specific goals and limitations of each organic production system.

Table 2. Functional groups of cover crops and their major ecological services in organic systems.

3.2 Functional traits and ecosystem services

A meta-analysis by Yousefi et al. (2024), spanning diverse cover crop taxa across agricultural landscapes including legumes, cereals, and brassicas, confirmed that cover crops deliver bundles of services simultaneously, including nutrient cycling, soil health improvement, weed suppression, and biodiversity support. However, individual service delivery is strongly species-dependent, reinforcing that cover crops should be selected as purpose-built tools matched to specific management objectives rather than deployed as generic fertility inputs. In a study comparing 15 species for orchard soil management, including common vetch (Vicia sativa), phacelia (Phacelia tanacetifolia), barley (Hordeum vulgare), oats (Avena sativa), crimson clover (Trifolium incarnatum), and subterranean clover (Trifolium subterraneum), large functional differences in biomass production, nitrogen accumulation, and root trait profiles were documented; such differences can determine which species is most appropriate for specific soil management objectives in organic perennial systems (Capri et al., 2023). Comparing legumes, grasses, brassicas, and their mixtures, Jones et al. (2025) found that both functional group identity and diversity influenced soil health outcomes, but that no single functional group was superior across all measured soil biological and physical indicators. These results underscore that mixture design must be tailored to the specific services being prioritized. Couedel et al. (2018) provided a landmark demonstration of mixture complementarity by testing crucifer-legume combinations, specifically winter radish (Raphanus sativus var. longipinnatus) or white mustard (Sinapis alba) grown with winter pea (Pisum sativum). These mixtures delivered effective simultaneous nitrate catch crop and green manure services that neither the crucifer nor the legume monoculture could achieve individually. A review synthesizing diverse cover crop treatments across multiple systems (Dutter et al., 2025) documented that improved soil health often coincided with neutral or negative cash crop yield responses when species choice or termination timing was not optimal, highlighting that mixture deployment does not necessarily resolve management trade-offs and that agronomic context should inform species selection decisions.

4 Effects of cover crops on soil health

4.1 Soil physical properties

A review of diverse legumes, cereal cover crops, and brassicas revealed that soil aggregate stability, water infiltration, and bulk density were improved when high-biomass species, especially winter rye (Secale cereale) and sorghum-sudan grass, were grown across multiple seasons. These species’ dense, fibrous root systems formed extensive biopore networks and provided copious organic inputs that fueled aggregate-binding microbial activity (Haruna et al., 2020). Blanco-Canqui and Ruis (2020) showed that improvements in soil physical condition were both management and time-dependent, with above-ground residue mass as a direct function of species choice and growing season length, which is the primary driver of soil surface protection from raindrop impact and erosive runoff. A meta-analysis of studies using legumes, cereals, and brassicas in different climates worldwide (Yan and Arthur, 2025) supported overall positive physical soil responses, such as increased aggregation, infiltration, and decreased bulk density, but with high variability depending on the species and climate; biomass-productive cereal species such as winter rye had stronger physical effects than low-biomass legumes. These physical improvements are also influenced by whether the residues are incorporated or retained on the soil surface, because surface mulch can reduce raindrop impact, erosion, crusting, evaporation, and compaction while frequent tillage can partially disrupt developing aggregates and fungal networks.

In the context of organic vegetables, Larkin (2024) compared the monoculture of winter rye (Secale cereale) to a six-species mixture of oats (Avena sativa), winter pea (Pisum sativum), fodder radish (Raphanus sativus), crimson clover (Trifolium incarnatum), phacelia (Phacelia tanacetifolia), and buckwheat (Fagopyrum esculentum) in organic production of snap bean, zucchini squash, and sweet pepper in Maine. Poor establishment of phacelia and buckwheat components under competitive or unfavourable early-season conditions reduced the total biomass and ground cover of the mixture below that of the winter rye monoculture, illustrating how establishment failure in a mixture can undermine the physical soil coverage benefits otherwise expected from species diversity. Working with legume-cereal mixtures including hairy vetch and winter rye, Gentsch et al. (2024) demonstrated that cover crops not only increase total soil organic carbon but also redistribute it toward macroaggregate fractions. This structural change enhances soil physical stability and reduces susceptibility to compaction and surface sealing. Nyabami et al. (2024), managing diverse cover crop species over three consecutive years in a subtropical vegetable system, found measurable increases in soil organic matter and labile carbon pools, which directly improved soil aggregate stability and water-holding capacity, with the magnitude of the physical improvements increasing progressively across the three seasons.

Wu et al. (2024) evaluated multiple cover crop species on the Canadian prairies over a three-year period and found that meaningful soil health responses, including physical indicators such as aggregate stability and bulk density, occurred even in colder climates. However, different indicators responded at different rates and magnitudes, reinforcing the idea that short, single-season trials in cold environments will consistently underestimate the long-term trajectory of physical soil improvement. Irmak et al. (2018) concluded across multiple reviews that the strongest physical responses were universally associated with species producing the highest above-ground biomass and most laterally extensive root systems, a functional profile that places winter rye, triticale, sorghum-sudan, and fodder radish at the top of the species selection hierarchy for physical soil health management in organic systems. In eggplant cultivation, Wojciechowski et al. (2012) found improvements in selected soil structure indicators under white clover (Trifolium repens) living mulch management. They attributed the improvements to the continuous root activity and organic matter additions maintained by the actively growing ground cover throughout the season.

4.2 Soil chemical properties

Reviewing evidence from multiple systems where cover cropping was repeated, Sharma et al. (2018) found that multiple repetitions of cover cropping increased soil organic carbon, total nitrogen, cation exchange capacity, and available phosphorus, with p^H buffering capacity improving alongside organic matter accumulation. In particular, leguminous species, such as hairy vetch (Vicia villosa) and crimson clover (Trifolium incarnatum), produced the greatest increases in mineral N, whereas grasses such as winter rye (Secale cereale) and oats (Avena sativa) resulted in larger carbon input effects because of their higher residue biomass and higher C:N ratios. Confirming the results across temperate systems, Scavo et al. (2022) found that combinations of legume and cereal functional groups produced the most consistent and broadest multi-parameter chemical soil improvements, as the combination of nitrogen from legume residues and carbon from cereal residues enhanced the soil organic matter.

Larkin (2024), working in certified organic vegetable production in Maine with winter rye (Secale cereale) monoculture and the six-species mixture described above, found that compost amendment rather than cover crop species alone produced the most reliable improvements in soil p^H, organic matter, and nutrient availability for snap bean, zucchini, and sweet pepper crops. The results underscore that in organic systems, chemical fertility management is most beneficial when cover crops are paired with complementary organic amendments rather than positioned as the sole fertility input. After three years of continuous cover crop management in a subtropical vegetable system, Nyabami et al. (2024) documented that labile carbon fractions’ mineral-associated and particulate organic matter increased in ways that directly improved soil nutrient retention and cation exchange capacity. This demonstrates that active organic matter fractions respond to cover cropping sooner than bulk soil organic carbon stocks and are therefore more sensitive indicators of management change. Bair et al. (2008) showed in a following-crop experiment that an incorporated crimson clover (Trifolium incarnatum) cover crop released substantial mineral nitrogen concentrated in the first four to six weeks. However, this release window had to coincide with cash crop establishment to avoid either nitrogen deficit or leaching loss, a timing constraint that has direct management implications for organic vegetable producers relying on legume residue nitrogen.

4.3 Soil biological properties

In a meta-analysis spanning diverse cover crop treatments including legumes, cereals, brassicas, and their mixtures, Kim et al. (2020) found that cover cropping consistently increased soil microbial biomass carbon and nitrogen, microbial diversity indices, and functional enzyme activity. The largest microbial biomass increases were associated with high-residue, nitrogen-rich legume treatments such as hairy vetch and crimson clover. In a complementary meta-analysis, Muhammad et al. (2021) confirmed increases in microbial biomass under cover crops spanning multiple functional groups. The study also documented shifts in microbial community structure, including increased fungal-to-bacterial ratios under high C:N cereal residues such as winter rye, with functional consequences for the rate and temporal pattern of nitrogen mineralization. A recent meta-analysis of different cover crop treatments (Lucia et al., 2025) confirmed positive average effects on microbial biomass and enzymatic activity but showed that responses were highly timing-sensitive. They were strongest during active residue decomposition and declined toward baseline without sustained annual cover crop inputs.

Biological soil health benefits in organic systems rely on multi-year management rather than episodic cover crop use. A study measuring the effects of different cover crop species composition treatments (legume-dominant, legume-mixed, grass-dominant, and grass-mixed) on soil bacterial communities in tomato rotation systems (Gao et al., 2022) found that the identity of the species deployed, not just the presence of any cover crop, determined the community structure, with legume-dominant and grass-dominant treatments producing significantly different community profiles. Castellano-Hinojosa and Strauss (2020) showed that in tree-crop systems, orchard cover crops (e.g., inter-row legumes and grasses) significantly altered microbial communities, with implications for nutrient cycling that differed from those in annual systems due to the permanent, layered soil environment created by established tree root systems. In citrus orchards with established orchard floor cover vegetation, Castellano-Hinojosa et al. (2023) found that cover crop effects on soil microbial communities and biological activity were vertically structured through the soil profile, with the uppermost 0–10 cm layer showing the strongest biological responses. Nakamoto and Tsukamoto (2006) found that long-term white clover management as a living mulch in maize fields significantly enhanced the population and activity of bacteria, fungi, and micro-arthropods across the soil profile relative to bare-soil or tillage-only control, developing a functionally active biological community that recycles nutrients effectively.

5 Cover crops and soil nutrient dynamics

5.1 Biological nitrogen fixation

Scavo et al. (2022) summarized nitrogen fixation in temperate organic systems across several legume species like common vetch (Vicia sativa), hairy vetch (Vicia villosa), faba bean (Vicia faba), crimson clover (Trifolium incarnatum), and white clover (Trifolium repens). They found that although the rate of fixation varied based on the quality of the rhizobial inoculum, the soil mineral nitrogen concentration at the time of establishment, and the length of the growing season, well-managed legume cover crops supplied 50 to 180 kg N ha^-¹ season^-¹. Fixed nitrogen interacts with the scavenging capacity of subsequent non-legume catch crops in rotation, forming a biological nitrogen cycle that can maintain organic fertility from season to season when species are intentionally sequenced (Thorup-Kristensen, 2001). In a subsequent follow-crop experiment with incorporated crimson clover (Trifolium incarnatum), Bair et al. (2008) demonstrated that while significant mineral nitrogen was available within four to six weeks after incorporation, the timing of release needed to coincide with cash crop establishment to produce a yield benefit. Vogeler et al. (2022) confirmed that the residue’s C:N ratio was the major factor controlling mineralization rate, with legume residues releasing nitrogen within weeks and grass residues delaying release for months. The study used multiple catch crop species, including hairy vetch (Vicia villosa) and white clover (Trifolium repens) as low-C:N species and winter rye (Secale cereale) and triticale as high-C:N species.

5.2 Nitrate scavenging by non-leguminous cover crops

In a comparison of cover crops with contrasting root architectures – fodder radish (Raphanus sativus), chicory (Cichorium intybus), Italian ryegrass (Lolium multiflorum), and white mustard (Sinapis alba) – Thorup-Kristensen (2001) found that the rooting depth and the rate of downward root extension were the most important traits determining the potential of a species to scavenge residual nitrate below 60 cm; deep-rooting fodder radish and chicory captured significantly more residual nitrate than the shallower-rooted ryegrass and mustard. In modeling and measuring nitrogen nutrition of crops after multiple catch crop species, Thorup-Kristensen (1994) found that species not only differed in the total amount of nitrogen they removed from the soil profile, but also in the proportion of nitrogen that was mineralized and available to the subsequent cash crop. This distinction is important for selecting catch crop species for fertility management objectives in organic rotations.

In a study using annual ryegrass (Lolium multiflorum), white mustard (Sinapis alba), and phacelia (Phacelia tanacetifolia) under reduced tillage conditions, Arlauskiene and Sarunaite (2023) noted that the release of nutrients from cover crop biomass to the soil was not equivalent to nutrient storage, with the timing and method of termination strongly modifying the proportion of captured nutrients that became available to the cash crop. Gentsch et al. (2021) compared winter-killed cover crops such as phacelia (Phacelia tanacetifolia) and buckwheat (Fagopyrum esculentum) and showed that these naturally killed species can impact nutrient retention and soil water dynamics over winter without additional spring termination operations, reducing management demand while still providing fertility services in temperate organic rotations.

5.3 Mixture strategies and phosphorus dynamics

Couedel et al. (2018) demonstrated that crucifer-legume mixtures of winter radish (Raphanus sativus var. longipinnatus) or white mustard (Sinapis alba) with winter pea (Pisum sativum) provided effective simultaneous nitrate catch crop and green manure services that neither the crucifer nor the legume monoculture alone could achieve. The crucifer scavenged deep residual nitrate, while the legume fixed atmospheric nitrogen, a functional complementarity directly relevant to organic rotation design. White clover (Trifolium repens) used as a living mulch in maize fields was shown by Deguchi et al. (2005) to enhance early phosphorus nutrition; mycorrhizal network extensions from the clover extended phosphorus uptake beyond the root zone of the maize crop. This finding was extended over several seasons by Deguchi et al. (2017), who showed that continuous white clover (Trifolium repens) living mulch management reduced the phosphorus fertilizer requirement in corn by enhancing the soil-biological phosphorus solubilization pathway. This finding has direct relevance to certified organic systems, which are limited to approved organic materials as sources of phosphorus. In a California walnut orchard with legume and mixed orchard floor cover crops, Curtright et al. (2025) quantified nitrogen provisioning and found that orchard floor cover crops can provide significant inputs of nitrogen to perennial tree systems. However, the timing of release relative to the trees’ demand windows is the key management variable for realizing a fertility benefit.

The major nutrient cycling pathways influenced by cover crop biomass and residue decomposition in organic cropping systems are depicted in the Figure 1. Legume cover crops contribute biologically fixed nitrogen, while non-leguminous species capture residual nitrate from deeper soil layers and reduce nutrient losses. After termination, residue decomposition controls the timing and rate of nutrient release, with low C legume residues generally mineralizing more rapidly and high C grass residues releasing nutrients more slowly. The figure also highlights that nutrient benefits depend on synchronizing cover crop decomposition with cash crop demand, as well as on species mixtures that combine nitrogen fixation, nitrate scavenging, and phosphorus-mobilizing functions.

6 Cover crops and soil organic matter

Cover crops add to soil organic matter through above-ground biomass residues, root exudates, root turnover, and microbial products formation in the rhizosphere. Root growth can promote aggregation, biopore formation, and biological activity, while residues retained on the soil surface protect the soil by reducing raindrop impact, runoff, erosion, surface crusting, and compaction risk. These surface-residue effects are especially important in vegetable systems where repeated tillage and low soil cover can accelerate soil degradation. Evidence from intensive vegetable farms in southern Uruguay shows that soil degradation is strongly associated with losses of soil organic carbon and structural stability, and that reduced tillage, cover crop residues, and organic matter inputs can improve water capture and reduce erosion in raised-bed vegetable systems (García de Souza et al., 2011; Alliaume et al., 2013, 2014). However, cover crop effects on soil organic carbon formation and long-term carbon balance should not be interpreted as automatic or uniform across sites. Legumes, such as hairy vetch (Vicia villosa) and crimson clover (Trifolium incarnatum), generate high-nitrogen, low-C:N residues that decompose quickly and mostly feed labile organic matter fractions; grasses, such as winter rye (Secale cereale) and triticale, produce more recalcitrant, high-C:N residues and larger, more extensive root systems that contribute more to stable mineral-associated organic matter pools (Scavo et al., 2022; Moukanni et al., 2022). Therefore, mixture design may influence not only total biomass but also the balance between short-term nutrient release and longer-term carbon stabilization (Connell et al., 2025).

Salisu et al. (2025) confirmed positive average effects of cover cropping on soil organic carbon and overall soil quality across a wide range of cover crop species, including legumes, cereals, brassicas, and their mixtures. In a subtropical vegetable system, Nyabami et al. (2024) reported that three years of cover crop management enhanced labile carbon pools and mineral-associated and particulate organic matter fractions before total soil organic carbon stocks were affected, in keeping with the idea that active carbon fractions are more sensitive early-season indicators of management change than bulk soil organic carbon. A global meta-analysis across 35 species in five climates showed that cover crop effects on soil organic carbon are positive and highly consistent across systems, but the magnitude of gains is strongly mediated by climate (Hao et al., 2023), which may be a key factor in setting realistic expectations for carbon management.

Two important corrective notes are warranted for organic producers and researchers interpreting this evidence base. In a review of evidence from a variety of cover crops, Chaplot and Smith (2023) argued that soil organic carbon stock gains have been overestimated in the literature, especially in studies of short duration or using methodologies that fail to adequately account for changes in bulk density and spatial variability. This was further supported by Moukanni et al. (2022), who showed that the long-term stability of carbon gains is strongly dependent on biomass quantity and quality, rooting depth, and management context (including tillage frequency), which can quickly negate accumulated carbon gains. The latter finding is especially important for organic systems that use periodic mechanical tillage for weed control, as the carbon accumulation benefits of high-biomass cover crops like winter rye (Secale cereale) or hairy vetch (Vicia villosa) can be partially negated by tillage-associated carbon oxidation during weed management operations. The functional importance of soil organic matter also links directly to ecological weed management. Cover crop biomass that contributes to soil organic matter can simultaneously function as a surface mulch, influencing weed emergence by reducing light availability, moderating soil temperature, maintaining surface moisture conditions, and creating a physical barrier to seedling establishment (Hartwig and Ammon, 2002; Osipitan et al., 2018; Navarro-Miró et al., 2019). Residue persistence is therefore important not only for carbon inputs, but also for weed suppression. High-C grass residues may provide longer-lasting mulch and stronger early-season weed suppression, whereas low-C legume residues may release nitrogen more rapidly but decompose too quickly to provide persistent soil cover. Thus, the same residue traits that influence soil organic matter formation also shape the duration and strength of weed suppression.

7 Weed suppression by cover crops

7.1 Mechanisms – mulching, competition, and allelopathy biotic regulation

Weed suppression by cover crops occurs through interacting biological and physical mechanisms. During growth, cover crops compete with weeds for light, space, water, and nutrients. After termination, surface residues reduce light transmission, buffer soil temperature, and create a physical barrier to emergence. Residues and root exudates can also contribute allelopathic effects, while increased soil cover and biological activity can influence seed predation, seed decay, and microbial interactions. Thus, weed suppression should be treated as a biological regulation function connected to soil ecology, not only as a biomass effect. However, these mechanisms vary with cover crop species, residue mass, termination timing, weed flora, and whether the cover crop is used as living mulch, green manure, or surface residue (Hartwig and Ammon, 2002; Baraibar et al., 2018a, 2018b; Osipitan et al., 2018).

Allelopathic suppression includes phytotoxic secondary metabolites released during decomposition of cover crop residue. In their study of ecological service-providing crops like brassica and legume species preceding melon, Ciaccia et al. (2015) showed that the allelopathic interactions between cover crops and weeds were combined with physical mulch effects, in which brassica species produced glucosinolate-derived isothiocyanate compounds that inhibited weed germination through biochemical pathways independent of physical residue. In field experiments, Menalled et al. (2023) found that while allelopathic weed suppression can be targeted through deliberate, phylogeny-informed cover crop selection, in some cases, phylogenetically related weed species were more strongly suppressed by specific cover crop treatments. This suggests that allelopathic weed suppression can be targeted through deliberate, phylogeny-informed cover crop selection – a finding with practical implications for organic weed management where weed community composition is known. Figure 2 illustrates the major mechanisms through which cover crop residues suppress weeds after termination. Surface residues act as a physical mulch by reducing light penetration, moderating soil temperature, and creating a barrier that limits weed seedling emergence. At the same time, decomposing residues may release allelopathic compounds that inhibit weed germination or early growth, while increased soil cover can also influence seed predation and microbial activity in the weed seed bank. Therefore, weed suppression by cover crops should be understood as the combined result of residue biomass, species-specific biochemical effects, and ecological interactions occurring at the soil surface.

7.2 Biomass, species, and climate as primary drivers

The single most significant factor for weed suppression across cover crop systems is biomass production. Greater weed suppression is associated with higher residue mass (Dong and Zeng, 2024; Baraibar et al., 2018a), although studies that measured both factors also found that species identity, on average, had greater effects on weed suppression than residue mass (Dong and Zeng, 2024). This makes choosing high biomass productivity species for weed suppression a preferred strategy. In field experiments comparing winter rye (Secale cereale), hairy vetch (Vicia villosa), and other common cover crop species, Baraibar et al. (2018b) showed that Growing Degree Day accumulation and species identity explained the outcomes of weed biomass under winter covers, with substantial year-to-year variability in suppression even under identical management. This is an important practical finding for organic producers, who cannot compensate for poor cover crop performance with herbicide application.

Baraibar et al. (2018a) compared monocultures of winter rye (Secale cereale), hairy vetch (Vicia villosa), Austrian winter pea (Pisum sativum subsp. arvense), canola (Brassica napus), and two- and three-species mixtures in field experiments. Weed suppression tracked total mixture biomass closely, and some mixtures outperformed individual monocultures by combining the physical mulch of winter rye with the competitive density of legumes. In a long-term Mediterranean field experiment, Restuccia et al. (2020) found that subterranean clover (Trifolium subterraneum) decreased weed biomass, viable weed seed bank density, and weed species richness compared with bare soil controls over multiple seasons, indicating species-specific cumulative weed community restructuring. In a study of herbicide-free wheat-potato rotations under conservation tillage, Schmidt et al. (2019) found that combining rye-pea (Secale cereale + Pisum sativum) and triticale-vetch (Tritico secale + Vicia sativa) mixtures with compost amendments inhibited the development of a significant weed seed bank relative to reduced tillage alone, illustrating that cover crops are most effective in delivering weed management when they are integrated into a carefully designed cropping system (i.e., the principle of integrated management).

7.3 Seed bank dynamics

Evidence from multiple cover crop taxa (winter rye, hairy vetch, and diverse mixtures) suggests that consistent and biomass-rich cover cropping can reduce total viable weed seed bank density and alter weed community composition over time, although these cumulative effects usually require at least three consecutive years of effective suppression to be statistically significant (Sias et al., 2021). In a long-term experiment with diverse cover crop treatments managed over multiple cropping cycles, Nichols et al. (2020) confirmed that seed bank composition shifted under cover crop management, but the direction and magnitude of change depended strongly on the specific weed community present and on the degree of management consistency across seasons. In horticultural systems, Westbrook et al. (2022) evaluated living mulch treatments, including white clover (Trifolium repens) and subterranean clover (Trifolium subterraneum), and found that living mulches reshaped weed community composition through selective competitive suppression, disproportionately reducing the most competitive weed species rather than simply reducing total weed numbers.

7.4 Weed suppression by cover crops in organic vegetable systems

Navarro-Miró et al. (2019) applied agroecological service crops hairy vetch (Vicia villosa), black oat (Avena strigose), and cereal rye (Secale cereale), managed with roller crimpers at several certified organic vegetable sites in Europe. They observed substantial reductions in weed density and weed species richness at all sites and pedo-climatic conditions, thus confirming the practical applicability of roller-crimped service crop residues for weed management in organic vegetable production in Europe. In a study of globe artichoke (Cynara cardunculus var. scolymus) production with subterranean clover (Trifolium subterraneum) as a living mulch in Puglia in southern Italy, Fracchiolla et al. (2022) reported that the locally adapted Brindisino ecotype suppressed weed cover to below 1% of ground area. This extremely effective result was achieved due to the dense, prostrate growth habit of the locally adapted genotype, whereas commercially produced subterranean clover varieties were not as effective. In certified organic broccoli raab (Brassica rapa) production using subterranean clover (Trifolium subterraneum) and white clover (Trifolium repens) as living mulches, subterranean clover showed the greatest weed suppression without a yield penalty, while white clover competed more with the broccoli raab when nutrients were limited (Fracchiolla et al., 2020). Based on a review of evidence from monocultures and mixtures of legumes, cereals, and brassicas, Fernando and Shrestha (2023) concluded that cover crops alone seldom achieve season-long weed control and are most effective when used as part of an integrated weed management system that includes rotation diversity and targeted mechanical treatments for weed escapes.

8 Cover crop termination strategies

Termination strategy plays a critical role in organic cover crop systems because it determines whether the residue is incorporated into the soil, retained on the surface, or managed as part of a reduced-tillage system. These different approaches directly influence residue decomposition, nutrient release, weed suppression, and crop establishment.

8.1 Mechanical incorporation

Incorporation by tillage also results in rapid residue decomposition, especially for low-C:N legume residues like hairy vetch (Vicia villosa) and faba bean (Vicia faba). This approach releases nitrogen faster than when residues are left on the soil surface, potentially making it available to transplanted vegetable crops at the critical establishment phase (Hefner et al., 2020). While its main agronomic benefit over surface retention is speed of nitrogen release, incorporation results in soil structural disruption, carbon oxidation, and the destruction of biological networks that have formed in the cover crop rhizosphere. For nitrogen-demanding vegetables with narrow establishment windows, incorporation of hairy vetch or crimson clover (Trifolium incarnatum) before transplanting is often the best way to match nitrogen release with cash crop demand (Hefner et al., 2020; Canali et al., 2015).

8.2 Roller crimping

In the most mechanistically informative comparison of roller-crimped versus incorporated cover crops, Hefner et al. (2020) used winter faba bean (Vicia faba), winter pea (Pisum sativum), hairy vetch (Vicia villosa), and two-way mixtures of each legume with winter rye (Secale cereale) in certified organic white cabbage production in Denmark. They found that roller crimping reduced total cabbage biomass and marketable yield relative to full incorporation in seasons where nitrogen was limiting due to the intact residue mat delaying its release from the legume fraction and reducing soil biological activity in the zone below the mulch barrier. This critical finding positions the suitability of roller crimping as directly dependent on the cover crop C:N ratio, the cash crop nitrogen demand, and the soil temperature at termination. It indicates that roller crimping is most appropriate for high-biomass, grass-dominant cover crops where weed suppression, rather than nitrogen supply, is the primary concern. In order to overcome the shortcomings of roller crimping alone, Frasconi et al. (2019) tested a combined roller crimper plus flaming strategy in herbicide-free no-till systems with hairy vetch (Vicia villosa) and cereal rye (Secale cereale) monocultures and mixtures and found that the combined termination method enhanced kill effectiveness for cover crop species that resprouted from the crown after crimping alone.

8.3 Termination timing and organic no-till

The duration of weed suppression and the pattern of nitrogen release from cover crop residues are both significantly influenced by the timing of termination in relation to the crop’s growth stage. Early flowering of hairy vetch (Vicia villosa), faba bean (Vicia faba), or crimson clover (Trifolium incarnatum) maximizes the labile fraction and speeds up nitrogen release; in high-C:N species like winter rye (Secale cereale), delaying to full anthesis or early seed-set maximizes biomass and mulch persistence but increases the risk of planting delay for the next cash crop (Canali et al., 2015). In a review of organic zero-tillage systems in the northern U.S. Great Plains, winter rye (Secale cereale), hairy vetch (Vicia villosa), and their mixtures were evaluated over several seasons. The results showed that weed management reliability, termination consistency across diverse weed communities, and nutrient release timing remained the three primary obstacles to wider adoption of organic no-till (Carr et al., 2012). For example, in organic onion production the cover crop mulch can suppress weeds in no-till, but onion establishment and yield depend strongly on mulch thickness and residue persistence (Vollmer et al. (2010). Peigné et al. (2007) reported that conservation tillage in organic farming can improve soil protection and biological activity through surface residue retention, but it can also make weed and nitrogen management more difficult. Similarly, Lowry et al. (2021) found that strip tillage with a cereal rye–hairy vetch cover crop mixture changed nitrogen availability and produced variable responses in organic sweet corn. More recently, the cover crop-based reduced tillage in onion systems can improve soil-health-related functions, but weed pressure, nitrogen availability, and yield gaps remain important concerns (Scarlato et al., 2024). Together, these studies indicate that cover crop-based reduced tillage should be treated as a distinct management pathway with both benefits and limitations, rather than being discussed as equivalent to green manure incorporation. Table 3 compares major termination approaches and shows how each method creates different balances between fertility, weed control, soil protection, and management risk. The results reflect that cover crop termination in organic systems requires substantially more precision than in conventional systems where herbicide backup is available for weed management failures.

Table 3. Cover crop termination strategies and their effects on residue placement, nutrient release, and weed suppression in organic systems.

9 Impacts on the productivity of organic cropping systems

9.1 Vegetable crops

Larkin (2024) studied the productivity of snap bean, zucchini squash, and sweet pepper in certified organic systems at the University of Maine Highmoor Farm and compared winter rye monoculture and a six-species mixture of oats, winter pea, fodder radish, crimson clover, phacelia, and buckwheat to a winter rye monoculture. The poor establishment of phacelia and buckwheat in the six-species mixture resulted in lower total biomass than the monoculture of winter rye in some of the plot replicates. The yield of the three cash crops was not significantly affected by the identity of the cover crop mixture, but rather by the application of compost amendments at 5 and 10 Mg ha^-¹ to improve soil p^H, organic matter content, and nutrient availability. The findings indicate that a diverse cover crop mixture is not necessarily better than a monoculture if the quality of establishment is poor and that cover crops should be seen as supplementary to, rather than as a replacement for, organic fertility management strategies.

Hefner et al. (2020) found that the interaction of cover crop species and termination method was key in determining marketable yield in certified organic white cabbage cultivation in Denmark. Winter faba bean (Vicia faba), winter pea (Pisum sativum), hairy vetch (Vicia villosa), and their mixtures with winter rye (Secale cereale) were examined, with these cover crops terminated either through roller crimping or full incorporation. When these legume-rye mixtures were roller crimped, the result was reduced marketable cabbage biomass and yield in seasons where nitrogen was limiting. By contrast, when they were fully incorporated, the result was increased cabbage biomass and yield. The incorporation enhanced soil nitrogen availability, while roller crimping delayed mineralization of the legume nitrogen fraction, creating a nitrogen deficit during cabbage establishment. When these mixtures were fully incorporated, the result was increased cabbage biomass and yield, similar to the results obtained in bare soil treatments; they enhanced soil nitrogen availability, unlike roller crimping, which delayed mineralization of the legume nitrogen fraction, thus creating a nitrogen deficit during cabbage establishment.

Thavarajah et al. (2019) found that cover crops grown before kale (Brassica oleracea var. sabellica) in certified organic cultivation, including legume and cereal species, influenced not only biomass yield but also the concentration of mineral elements in the leaves. The results reflect how cover crop-driven changes in soil nutrient cycling directly affect crop nutritional quality. Another study found that tomato yield and soil fertility improved under cover crop plus organic mulch systems, particularly with crimson clover and rye-vetch mixtures, demonstrating that combining legume-derived nitrogen inputs with surface mulch can enhance both productivity and soil organic matter (Wang et al., 2009). Belfry et al. (2017) showed that hairy vetch and vetch-rye mixtures increased nitrogen availability and improved tomato yields, whereas winter rye alone sometimes reduced nitrogen availability due to temporary immobilization after incorporation. Long-term use of diverse cover crops led to cumulative soil health improvements and more stable, higher-quality tomato yields, in contrast to the variable outcomes often seen in short-term studies (Van Eerd et al., 2025). In maize-tomato systems, cover crop-based organic management achieved yields comparable to conventional systems while providing greater stability under drought conditions (Li et al., 2019).

In certified organic zucchini production, common vetch used as green manure or mulch improved at least one yield or quality parameter, such as fresh weight, dry matter, or sugar content, when combined with appropriate fertilization (Montemurro et al., 2013). Roller-crimped hairy vetch reduced early weed pressure but produced variable yields depending on biomass levels and the timing of nitrogen release relative to crop demand (Ciaccia et al., 2016). Montemurro et al. (2025) found that integrating cover crop management with adjusted fertilization rates resulted in more consistent and sustainable yields, reinforcing that cover crops and fertilizers function best as complementary inputs. Bruce et al. (2022a) reported that living mulch systems reduced weeds and insect pests, although careful management of competition, irrigation, and mulch density was necessary to avoid yield penalties.

In organic broccoli raab production, subterranean clover provided effective weed control without reducing yield, particularly when combined with higher fertilization rates, whereas white clover imposed stronger competition under nutrient-limited conditions (Fracchiolla et al., 2020). In cucurbit systems, both disease incidence and crop productivity depended on the interaction between cover crops and tillage practices, with nitrogen availability from hairy vetch playing a key role in determining yield outcomes (Bruce et al., 2022b).

9.2 Fruit crops

In apple orchards, Sharifi et al. (2016) examined the management of orchard floor cover crops, including clover mixtures, grass-legume combinations, and mixed vegetation, showing that these cover crops influenced both fruit yield and the concentrations of leaf nitrogen and mineral micronutrients. These results demonstrate that orchard floor management plays a direct role in shaping tree nutritional status through soil biological processes, rather than functioning solely as a means of ground cover or erosion control. Similarly, Giacalone et al. (2021) reviewed the effects of cover crops on quality and sustainability in perennial fruit orchards, including systems using grasses, legumes, and mixed inter-row vegetation in apple, pear, peach, and citrus production. The findings indicate that cover crops generally improve soil health, enhance habitats for beneficial arthropods, and can contribute to fruit quality, although these benefits are strongly influenced by water availability and irrigation practices, particularly under Mediterranean climatic conditions.

In viticulture, Abad et al. (2021) conducted a comprehensive review of cover crop use across global wine and table grape production systems, reporting consistent improvements in soil physical structure and biological activity associated with grass-legume mixtures and managed inter-row vegetation. However, they also highlighted the potential for competition between cover crops and vines for water and nutrients, especially in rainfed systems common in southern Europe. Further work by Abad et al. (2023) demonstrated that under-vine cover crops, including both grasses and broadleaf species, improved soil physical properties and biological activity in highly compacted and structurally degraded zones directly beneath the vine canopy. Studying a table grape vineyard in southern Italy, Gattullo et al. (2020), found that both spontaneous vegetation and sown inter-row cover crops significantly influenced soil organic matter, enzymatic activity, and grape production, with the amount of inter-row biomass identified as a key factor driving soil health improvements. Additionally, Sharifi et al. (2024) demonstrated, through greenhouse screening of multiple species such as clovers, vetches, and cereal grasses, substantial variation in nitrogen uptake and carbon sequestration potential among cover crops, supporting a trait-based approach for selecting suitable species in organic vineyard management prior to field implementation.

In citrus orchards, Silwana et al. (2023) reviewed the use of cover crops, including legumes, grasses, and mixed vegetation, across different citrus-producing regions and found increasing evidence of their benefits for soil health, nutrient cycling, and ecological functioning. However, they also noted that the available literature remains limited and that more research is needed before making robust species-specific recommendations. Castellano-Hinojosa et al. (2023) provided further mechanistic insights by showing that the effects of cover crops on microbial communities, nutrient cycling enzymes, and soil nutrient distribution vary significantly with soil depth, particularly between the 0–10 cm and 10–30 cm layers. The findings highlight that shallow-rooted species primarily influence surface soil processes, whereas deep-rooted species such as fodder radish (Raphanus sativus) can affect nutrient dynamics throughout the active root zone of citrus trees. Capri et al. (2023) documented substantial differences in biomass production, nitrogen accumulation, and root architecture among 15 different cover crop species, including sainfoin, common vetch, phacelia, barley, oats, and various clovers. These results support the adoption of a trait-based, rather than generalized, approach to cover crop selection in organic perennial orchard systems.

9.3 Herb and specialty crops

A study comparing two contrasting living mulch species, berseem clover (Trifolium alexandrinum) and barley (Hordeum vulgare), in certified organic black cumin (Nigella sativa L.) production on salt-affected soils in Iran (Benakashani et al., 2025) found that berseem clover significantly reduced weed density and increased black cumin seed oil yield while maintaining or improving seed lipid quality. The outcomes were attributed to the nitrogen-fixing capacity of the clover and its moderate competitive interaction with the small-seeded herb crop. In contrast, barley as a living mulch created unfavorable conditions for black cumin, suppressing rather than supporting the crop, due to intense early interspecific competition driven by its rapid establishment and vigorous growth. This demonstrates that legume species with moderate competitiveness are more suitable for small-seeded herb crops than aggressive cereal species that dominate light and nutrient resources early in the growth cycle. Fracchiolla et al. (2022) evaluated subterranean clover (Trifolium subterraneum), specifically the locally adapted Brindisino ecotype, as a living mulch in globe artichoke (Cynara cardunculus var. scolymus) production in southern Italy. They found that artichoke bud yield, averaging approximately 16 buds per plant, was not significantly reduced by the living mulch, while weed cover was suppressed to below 1%. These findings highlight that selection at the ecotype level can be as critical as species selection in living mulch systems; locally adapted ecotypes with prostrate and dense growth habits can provide strong weed suppression without compromising crop yield.

Bozzolo et al. (2025) compared multiple systems in certified organic globe artichoke production in California, including white clover living mulch, crimson clover cover crop, a buckwheat-pea mixture, and plastic mulch. White clover improved soil organic matter, active carbon fractions, and water infiltration; however, it reduced artichoke yield due to competitive effects. Crimson clover provided effective early-season weed suppression, but its benefits declined sharply after senescence, resulting in a mid-season weed control gap. These contrasting outcomes demonstrate that the species most beneficial for soil health may not be optimal for maximizing yield, and that the temporal dynamics of cover crop growth and senescence must be carefully managed in specialty cropping systems. Montemurro et al. (2020) examined the energetic implications of using cover crops as living mulches in Mediterranean organic systems, showing that such practices influence labor requirements, energy inputs, and net energy balance, thereby affecting overall system sustainability beyond agronomic performance. In a subsequent study, Montemurro et al. (2025) demonstrated that integrating legume-based cover crop management with adjusted organic fertilization rates in zucchini production resulted in more consistent and productive outcomes than either strategy alone, reinforcing the complementary roles of cover crops and fertilization.

9.4 Ornamental and nursery crops

Panth et al. (2020) evaluated winter cover crops in woody ornamental nursery systems, using small-grain cereals and their mixtures to suppress soilborne pathogens such as Phytophthora cinnamomi and Pythium spp. Their results showed that cover crops reduced disease severity and pathogen presence while increasing populations of beneficial fluorescent pseudomonads with known biocontrol properties. Importantly, these benefits were achieved without negatively affecting maple growth, indicating that biological disease suppression can be enhanced without compromising plant productivity, an especially valuable outcome in organic nursery systems with limited fungicide options. Parajuli et al. (2022) expanded this work by evaluating cereal, legume, and brassica cover crops for soilborne disease management, confirming that diverse cover crops can suppress pathogens through combined physical, biological, and allelopathic mechanisms. They also emphasized that research in ornamental nursery systems remains underdeveloped despite its clear potential. Parajuli et al. (2024) further demonstrated that cover crop mixtures often provide broader-spectrum disease suppression than monocultures, an important consideration for organic systems dealing with multiple pathogen pressures simultaneously.

Finally, Deguchi et al. (2007) provided mechanistic insight into how living mulches can enhance crop productivity. In silage corn systems, white clover (Trifolium repens) living mulch increased corn yield by promoting colonization of roots by arbuscular mycorrhizal fungi. This pathway operates independently of nitrogen supply and is particularly relevant in organic systems, where phosphorus availability is often limiting and mycorrhizal associations play a key role in nutrient acquisition efficiency. Cover crop recommendations must also be adjusted to the crop system because vegetables, orchards, vineyards, herbs, specialty crops, ornamentals, and nursery systems differ in planting windows, rooting depth, water demand, and tolerance to competition. For example, organic vegetable systems often require careful nutrient synchrony and weed suppression, while orchards and vineyards may benefit from inter-row or alley cover crops but face greater risks of water and nutrient competition. Table 4 summarizes crop-system-specific considerations and reinforces the need to align cover crop strategy with crop type, production timing, water availability, and management capacity.

Table 4. Crop-system-specific considerations for cover crop integration in organic production.

Productivity responses in organic systems should be interpreted through common mechanisms rather than by crop type alone. Across studies, yield benefits are most likely when cover crops improve nitrogen availability, suppress early weed pressure, protect soil structure, or improve water relations in ways that match the cash crop’s establishment window and nutrient demand. Yield penalties are most likely when high-C:N residues immobilize nitrogen, surface mulch delays soil warming, living mulches compete with the crop, or termination fails. Therefore, this section synthesizes vegetable evidence through mechanism-based pathways while retaining crop-specific examples as support.

Figure 3 provides a seasonal overview of how cover crops are integrated into organic cropping systems from establishment through termination and subsequent cash crop production. This timeline helps connect the findings summarized in this section by showing that cover crop effects on productivity depend not only on species selection, but also on planting time, biomass development, termination method, nutrient release, and the timing of cash crop establishment. Therefore, the productivity outcomes observed across vegetable, fruit, herb, and specialty crops should be interpreted as the result of coordinated seasonal management rather than the presence of cover crops alone.

10 Challenges and trade-offs

Although cover crops provide multiple ecosystem services, their benefits are not automatic and must be interpreted together with possible trade-offs. Nitrogen fixation, nitrate scavenging, weed suppression, soil physical improvement, soil organic carbon accumulation, and crop productivity benefits all depend on cover crop species, biomass production, residue quality, climate, soil condition, and termination timing. Table 5 presents these major services alongside their limitations, emphasizing that successful cover crop management requires matching the cover crop function with cash crop demand and local production constraints.

Table 5. Major ecosystem services and trade-offs associated with cover crop use in organic crop production systems.

10.1 Nitrogen immobilization

The most commonly reported agronomic risk associated with cover cropping in organic systems is the temporary immobilization of nitrogen during the decomposition of residues with a high C:N ratio, particularly from non-leguminous species. This risk becomes especially pronounced when residues from crops such as winter rye (Secale cereale), triticale, or sorghum-sudan are incorporated into the soil under cool or dry conditions that limit microbial activity. It is further exacerbated when a transplanted vegetable crop is planted shortly after termination, leaving a narrow window for nitrogen mineralization and uptake (Hefner et al., 2020; Osterholz et al., 2021). Clear experimental evidence of this phenomenon was seen in a study of certified organic white cabbage systems following a hairy vetch-winter rye (Vicia villosa + Secale cereale) mixture (Hefner et al., 2020). When the cover crop was terminated using a roller-crimper, the resulting intact mulch layer delayed nitrogen release from the legume component, leading to reduced cabbage yield in some seasons. In contrast, when the same mixture was incorporated into the soil, nitrogen availability increased, and crop yields improved. These findings demonstrate that the interaction between termination method and residue chemistry plays a decisive role in determining whether a cover crop enhances or constrains crop performance during the critical establishment phase.

10.2 Water competition

Another key challenge associated with cover cropping is competition for soil water. High-biomass cereal cover crops, particularly winter rye and triticale, have substantial water demands and extensive root systems that can significantly deplete soil moisture during their growth period. If termination is not timed to allow sufficient soil water recharging before planting the subsequent crop, the result can be reduced water availability, negatively affecting crop performance (Carr et al., 2012; Dutter et al., 2025). In their review of viticulture systems across Mediterranean regions, Abad et al. (2021) identified water competition as the primary limitation to cover crop adoption in rainfed vineyards, where water availability during the growing season is a critical determinant of grape yield and quality. Their comparison of grass monocultures, legume monocultures, and mixed systems showed that while cover crops provide soil and ecological benefits, their water use can offset these advantages under water-limited conditions. Similarly, Montemurro et al. (2020) demonstrated that living mulch systems alter not only water dynamics but also overall system energy use, indicating that their effects extend beyond simple crop competition and must be evaluated within a broader systems framework.

10.3 Management complexity and economic considerations

The adoption of cover crops in organic systems is also constrained by management complexity and economic considerations. Schoolman and Arbuckle (2022) highlighted that specialty crop producers, including those growing fruits, vegetables, and herbs, face unique logistical challenges compared to broad-acre crop producers. These include more complex and varied production schedules, limitations in equipment compatibility with standard cover cropping practices, and reduced access to specialized agronomic support for integrating cover crops effectively. In a survey of certified organic vegetable producers in Wisconsin, Moore et al. (2016) found that the intensity of cover crop use measured by frequency and species diversity was influenced more by farmers’ management experience and operational capacity than by their awareness of the benefits of cover cropping – underscoring that barriers to adoption are not solely technical but also institutional and experiential.

Dutter et al. (2025) further identified a recurring trade-off in which improvements in soil health indicators do not always translate into yield gains and may even result in neutral or negative yield outcomes, particularly in systems dominated by high-C:N residues, such as winter rye, that promote nitrogen immobilization. These trade-offs highlight the importance of incorporating economic analysis into evaluations of cover cropping, as improved soil function does not automatically equate to increased profitability. To address this complexity, Jian et al. (2020a) developed a decision-support tool that allows organic producers to estimate the potential impacts of cover crops on soil health and productivity under specific management conditions. This tool is based on a large global dataset (Jian et al., 2020b) and reflects the wide variability in cover crop performance across species, environments, and management systems. Recent meta-analyses indicate that these benefits are generally scalable across agroclimatic zones, although the magnitude and direction of individual responses are heavily dependent on species identity, management intensity, and site-specific soil conditions (Jones et al., 2025; Yan and Arthur, 2025).

11 Knowledge gaps and future research directions

The organic agriculture sector is expanding rapidly, and this growth underscores the need for a stronger certified organic-specific evidence base to guide cover crop management. Broader international reports, including FiBL/IFOAM statistics, show that organic agriculture has become a major global production and market sector, while U.S. market data from OTA and USDA NASS provide one important regional example of this expansion. However, the research needs identified here are global because organic systems differ widely in climate, water availability, labor access, certification rules, soil conditions, and crop calendars. First, there is a clear shortage of studies conducted under certified organic management conditions. Most existing research has been carried out in conventional systems, where factors like soil fertility status, weed dynamics, and management histories differ substantially from those in organic production. As a result, findings cannot always be directly applied to organic systems. Osterholz et al. (2021) identified interactions between cover crops and tillage as a major unresolved issue in organic agriculture, while Das et al. (2022) emphasized the need for studies that explicitly examine how cover crops interact with compost inputs, crop rotation diversity, and varying tillage intensities in organic vegetable systems. Second, long-term experimental data remains limited across cropping systems. Third, reduced-tillage organic systems that rely on roller-crimped, mowed, undercut, or winter killed cover crops represent a key research frontier because weed control, termination reliability, equipment access, nitrogen synchrony, water use vary strongly by region. Canali et al. (2015), working with hairy vetch, cereal rye, and their mixtures in Mediterranean vegetable systems, identified nitrogen synchrony and weed control as the main constraints. Fourth, future work should be more consistently include perennial systems, orchards, vineyards, herb crops, ornamentals, and diversified small farms, which remain underrepresented relative to annual vegetable and field crop systems. Fifth, climate adaptation of cover crop systems is an emerging priority. Changes such as warmer winters, which may alter biomass production of winter cereals, and increased summer drought frequency, which can intensify water competition from living mulches, require targeted research. Hao et al. (2023) has confirmed through a global meta-analysis that climate strongly influences soil responses to cover crops, making climate-specific management strategies essential rather than optional as organic agriculture expands into diverse environments.

In conclusion, cover crops strengthen organic production systems, their value depends on matching species traits and management pathways to specific system goals. Incorporating cover crops improves soil physical structure, supports nutrient cycling, stimulates biological activity, regulates weeds, and contributes to organic matter formation. Other benefits include nitrogen immobilization, water competition, delayed planting, incomplete termination, weed escape, and management costs. Cover crops are universally beneficial as multifunctional ecological regulators when selected and managed in relation to crop demand, residue placement, tillage intensity, soil condition, and local climate. Further research requires long-term, certified-organic, regionally adapted studies that integrate soil health, weed ecology, crop productivity, and economic outcomes into practical decision-support frameworks for organic producers.

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Footnotes

Edited by: Peter Ojiambo, North Carolina State University, United States

Reviewed by: Mariana Scarlato, Universidad de la República, Uruguay

Khulan Sharavdorj, Mongolian Academy of Sciences (MAS), Mongolia