In agriculture, cover crops are plants that are planted to cover the soil rather than for the purpose of being harvested. Cover crops manage soil erosion, soil fertility, soil quality, water, weeds, pests, diseases, biodiversity and wildlife in an agroecosystem—an ecological system managed and shaped by humans. Cover crops can increase microbial activity in the soil, which has a positive effect on nitrogen availability, nitrogen uptake in target crops, and crop yields. Cover crops reduce water pollution risks and remove CO₂ from the atmosphere. Cover crops may be an off-season crop planted after harvesting the cash crop. Cover crops are nurse crops in that they increase the survival of the main crop being harvested, and are often grown over the winter.

Although cover crops can perform multiple functions in an agroecosystem simultaneously, they are often grown for the sole purpose of preventing soil erosion. Soil erosion is a process that can irreparably reduce the productive capacity of an agroecosystem. Cover crops reduce soil loss by improving soil structure and increasing infiltration, protecting the soil surface, scattering raindrop energy, and reducing the velocity of the movement of water over the soil surface. Dense cover crop stands physically slow down the velocity of rainfall before it contacts the soil surface, preventing soil splashing and erosive surface runoff. Additionally, vast cover crop root networks help anchor the soil in place and increase soil porosity, producing suitable habitat networks for soil macrofauna. It keeps the enrichment of the soil good for the next few years.

One of the primary uses of cover crops is to increase soil fertility. These types of cover crops are referred to as "green manure". They are used to manage a range of soil macronutrients and micronutrients. Of the various nutrients, the impact that cover crops have on nitrogen management has received the most attention from researchers and farmers because nitrogen is often the most limiting nutrient in crop production.

Often, green manure crops are grown for a specific period, and then plowed under before reaching full maturity to improve soil fertility and quality. The stalks left block the soil from being eroded.

Green manure crops are commonly leguminous, meaning they are part of the pea family, Fabaceae. This family is unique in that all of the species in it set pods, such as bean, lentil, lupins and alfalfa. Leguminous cover crops are typically high in nitrogen and can often provide the required quantity of nitrogen for crop production. In conventional farming, this nitrogen is typically applied in chemical fertilizer form. In organic farming, nitrogen inputs may take the form of organic fertilizers, compost, cover crop seed, and fixation by legume cover crops. This quality of cover crops is called fertilizer replacement value.

Another quality unique to leguminous cover crops is that they form symbiotic relationships with the rhizobial bacteria that reside in legume root nodules. Lupins is nodulated by the soil microorganism Bradyrhizobium sp. (Lupinus). Bradyrhizobia are encountered as microsymbionts in other leguminous crops (Argyrolobium, Lotus, Ornithopus, Acacia, Lupinus) of Mediterranean origin. These bacteria convert biologically unavailable atmospheric nitrogen gas (N
₂) to biologically available ammonium (NH⁺
₄) through the process of biological nitrogen fixation. In general, cover crops increase soil microbial activity, which has a positive effect on nitrogen availability in the soil, nitrogen uptake in target crops, and crop yields.

Prior to the advent of the Haber–Bosch process, an energy-intensive method developed to carry out industrial nitrogen fixation and create chemical nitrogen fertilizer, most nitrogen introduced to ecosystems arose through biological nitrogen fixation. Some scientists believe that widespread biological nitrogen fixation, achieved mainly through the use of cover crops, is the only alternative to industrial nitrogen fixation in the effort to maintain or increase future food production levels. Industrial nitrogen fixation has been criticized as an unsustainable source of nitrogen for food production due to its reliance on fossil fuel energy and the environmental impacts associated with chemical nitrogen fertilizer use in agriculture. Such widespread environmental impacts include nitrogen fertilizer losses into waterways, which can lead to eutrophication (nutrient loading) and ensuing hypoxia (oxygen depletion) of large bodies of water.

An example of this is in the Mississippi Valley Basin, where years of fertilizer nitrogen loading into the watershed from agricultural production have resulted in an annual summer hypoxic "dead zone" off the Gulf of Mexico that reached an area of over 22,000 square kilometres (8,500 sq mi) in 2017. The ecological complexity of marine life in this zone has been diminishing as a consequence.