Agricultural management can have lasting impacts on microbial community structure and function. Consequent changes in biotic (i.e., plant inputs) and abiotic factors (i.e., soil fertility) due to agricultural management directly influence microbial community structure and function in soils. The goal of this study was to investigate the impact of long-term crop diversity on microbial communities and disease suppressive functional potential in soils. In 2012, we collected soil samples from the Biodiversity Gradient Experiment (established in 2000) at the Kellogg Biological Station LTER, Michigan State University. At this long-term experiment, crop diversity is manipulated, ranging from monoculture to a five species crop rotation. We sampled 7 treatments along the crop diversity gradient and a spring fallow treatment. Using molecular techniques, we examined the influence of crop diversity on total bacterial community composition (16S rRNA amplicon sequencing) and a subset of microbes capable of producing antifungal compounds (2,4-diacetylphloroglucinol: phlD gene fingerprint analysis; pyrrolnitrin: prnD gene quantitative PCR). The crop diversity treatment significantly influenced bacterial community composition and a subset of microbial communities associated with disease suppression of soil-borne fungal pathogens. In addition, cover crop biomass significantly contributed to variation in bacterial community composition. Plants and microbes drive nutrient cycling in this long-term crop diversity since no additional synthetic or organic amendments are applied. Variation in plant contributions to soil organic matter pools may be a possible mechanism driving shifts in microbial community patterns and disease suppressive functional potential.