Microarthropods, largely collembola and mites, are often the most numerous and diverse arthropods living in soils globally. While their direct impacts on nutrient cycling are relatively modest, recent studies show they can have strong indirect influences on soil carbon dynamics. As soils are the largest reservoir of terrestrial carbon, understanding the effects of microarthropods may have important implications for promoting soil accrual, particularly in managed ecosystems, but the effects of agronomic management practices on microarthropod community structure are not straight forward. Crop cultivation drastically alters soil conditions. While microarthropods generally respond negatively to agricultural intensification, the varying responses of different microarthropod groups complicate our understanding of how management influences microarthropod communities and their impacts on carbon dynamics. We surveyed microarthropods from three bioenergy cropping systems: an annual monoculture, a perennial monoculture, and a perennial polyculture. While populations showed high variation within and between sampling years, our results suggest that perennial bioenergy cropping systems support higher microarthropod abundances and diversity, but microarthropod groups with differing life history strategies exhibit contrasting responses. A better understanding of how microarthropod communities are structured within different bioenergy cropping systems will help us understand their interactions with microbes and plants, with potentially important impacts on soil carbon dynamics.