Cover crops are commonly grown to enhance soil quality by building and maintaining soil organic matter and facilitating a biotic community that enhances crop productivity and resistance and resilience to stress. The physical enhancement of soils not only protects them from erosion, but also improves habitat quality of soil biota which include a wide array of organisms. In addition to their indirect influence on soil biology exerted through their effect on soil quality, cover crops directly benefit crop production by increasing the abundance and effectiveness of N2 fixing rhizobacteria, arbuscular mycorrhizae, plant growth promoting bacteria, or endophytes that can suppress disease varies with cover crop type and management. As we gain insights into how cover crops influence soil food webs, and shape the microbial community we will increase our ability to leverage alliances between plants and soil biota to increase agricultural sustainability.