Microbiomes can aid in the protection of hosts from infection and disease, but the mechanisms underpinning these functions in complex environmental systems remain unresolved. Soils contain microbiomes that influence plant performance, including their susceptibility to disease. For example, some soil microorganisms produce antimicrobial compounds that suppress the growth of plant pathogens, which can provide benefits for sustainable agricultural management. Evidence shows that crop rotations increase soil fertility and tend to promote microbial diversity, and it has been hypothesized that crop rotations can enhance disease suppressive capacity, either through the influence of plant diversity impacting soil bacterial composition or through the increased abundance of disease suppressive microorganisms. In this study, we used a long‐term field experiment to test the effects of crop diversity through time (i.e., rotations) on soil microbial diversity and disease suppressive capacity. We sampled soil from seven treatments along a crop diversity gradient (from monoculture to five crop species rotation) and a spring fallow (non‐crop) treatment to examine crop diversity influence on soil microbiomes including bacteria that are capable of producing antifungal compounds. Crop diversity significantly influenced bacterial community composition, where the most diverse cropping systems with cover crops and fallow differed from bacterial communities in the 1–3 crop species diversity treatments. While soil bacterial diversity was about 4% lower in the most diverse crop rotation (corn–soybean–wheat + 2 cover crops) compared to monoculture corn, crop diversity increased disease suppressive functional group prnD gene abundance in the more diverse rotation by about 9% compared to monocultures. In addition, disease suppressive potential was significantly diminished in the (non‐crop) fallow treatment compared to the most diverse crop rotation treatments. The composition of the microbial community could be more important than diversity to disease suppressive function in our study. Identifying patterns in microbial diversity and ecosystem function relationships can provide insight into microbiome management, which will require manipulating soil nutrients and resources mediated through plant diversity.