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Growing a cover crop between main crops imitates natural ecosystems where the soil is continuously covered with vegetation. This is an important management practice in preserving soil nutrient resources and reducing nitrogen (N) losses to waters. Cover crops also provide other functions that are important for the resilience and long-term stability of cropping systems, such as reduced erosion, increased soil fertility, carbon sequestration, increased soil phosphorus (P) availability, and suppression of weeds and pathogens. Much is known about how to use cover crops to reduce N leaching, for climates where there is a water surplus outside the growing season. Non-legume cover crops reduce N leaching by 20%–80% and legumes reduce it by, on average, 23%. There are both synergies and possible conflicts between different environmental and production aspects that should be considered when developing efficient and multifunctional cover crop systems, but contradictions about different functions provided by cover crops can sometimes be overcome with site-specific adaptation of measures. One example is cover crop effects on P losses. Cover crops reduce losses of total P, but extract soil P to available forms and may increase losses of dissolved P. How to use this effect to increase soil P availability on subtropical soils needs further studies. Knowledge and examples of how to maximize the positive effects of cover crops on cropping systems are improving, thereby increasing the sustainability of agriculture. One example is combined weed suppression in order to reduce dependence on herbicides or intensive mechanical treatment.