The abundance and distribution of soil microbial populations, i.e., microbial diversity is widely promoted as a key tenant of sustainable agricultural practices and/or soil health. A common approach to describing microbial diversity is phylogenetic analysis with high-throughput sequencing of microbial DNA. However, owing to the tremendous amounts of data generated, a continuing effort is required to better assess the effects of agricultural management systems on soil microbial diversity. Here, we report on the combined effects of management systems on bacterial and fungal diversity in a loessal agricultural soil located in north-central Mississippi, USA. Amplicon sequencing was performed using 16S rRNA-gene and ITS2 from soil samples collected from a three-year study with combinations of maize-soybean crop rotation, tillage practices, and winter vegetative covers. Differences were found in microbial fungal β-diversity among the management systems, with distinct clustering patterns for no-tillage combined with either winter weeds or bare-fallow. Management systems showed a significant influence on soil pH and bulk density, which were positively correlated with fungal community composition. Developments in the description and interpretation of soil microbial diversity will contribute to a more accurate understanding of its role in the various functions and processes important to agricultural soil management.