Field trials were conducted from 2010 to 2013 at four locations in Illinois to evaluate the impact of cover crops (cereal rye [Secale cereal], brown mustard [Brassica juncea], winter canola [B. napus], and winter rapeseed [B. napus]) on soybean [Glycine max] stands and yield, diseases, pathogen populations, and soil microbial communities. Cover crops were established in the fall each year and terminated the following spring either by using an herbicide (no-till farms), by incorporation (organic farm), or by an herbicide followed by incorporation (research farm). Although shifts in soilborne pathogen populations and microbial community structure were not detected, cover crops were found to induce general soil suppressiveness in some circumstances. Cereal rye and rapeseed improved soybean stands in plots inoculated with Rhizoctonia solani and decreased levels of soybean cyst nematode in the soil. Cereal rye increased soil suppressiveness to R. solani and Fusarium virguliforme, as measured in greenhouse bioassays. Cereal rye significantly improved yield when Rhizoctonia root rot was a problem.