Cover cropping is proposed to enhance soil microbial diversity and activity, with cover crop type affecting microbial groups in different ways. We compared fungal community compositions of bulk soils differing by cover crop treatment, season, and edaphic properties in the third year of an organic, conventionally tilled rotation of corn-soybean-wheat planted with winter cover crops. We used Illumina amplicon sequencing fungal assemblages to evaluate effects of nine treatments, each replicated four times, consisting of six single winter cover crop species, a three-species mixture, a six-species mixture, and fallow. Alpha-diversity of fungal communities was not affected by cover crop species identity, function, or diversity. Sampling season influenced community composition as well as genus-level abundances of arbuscular mycorrhizal (AM) fungi. Cover crop mixtures, specifically the three-species mixture, had distinct AM fungal community compositions, while cereal rye and forage radish monocultures had unique Core OTU compositions. Soil texture, pH, permanganate oxidizable carbon, and chemical properties including Cu, and P were important variables in models of fungal OTU distributions across groupings. These results showed how fungal composition and potential functions were shaped by cover crop treatment as well as soil heterogeneity.Microbial diversity is an important aspect of soil health, as soil microbial communities mediate many biogeochemical processes and are sensitive to disturbances that can lead to long-lasting ecosystem effects 1 . Greater richness and evenness in the representation of bacteria and fungi in soils can help mitigate plant responses to environmental stressors 2 . With the advent of high-throughput DNA sequencing technologies that allow for more detailed genetic information, we can determine if and how microbial compositions shift in response to disturbance and edaphic differences and, to some degree, what those changes may mean for ecosystem processes.Cover cropping is the practice of growing ground-covering crops during the intervals between successive cash crops. Cover cropping imparts numerous benefits to soil, including the addition of organic carbon (C) from roots, root exudates, and aboveground residues and the improvement of soil structure and tilth 3-5 . Ecosystem services provided by cover crops include protection from soil erosion, enhanced soil water-holding capacity, reduced weed colonization and growth, plant resilience to pathogens and increased crop yield 5,6 . Legume cover crops provide biologically fixed nitrogen (N), while grasses take up excess soil inorganic N and improve N retention. A complete suite of ecosystem services is not deliverable by any one cover crop species. Thus, planting mixtures of cover crops has been proposed as a means to provide varied combinations of ecosystem services based on the functional traits of individual cover crop species 5,7-10 .Cover crops may alter microbial community diversity and function by varying the types and composition of exuded C...