Several studies investigating the role of arbuscular mycorrhizal (AM) fungi in plant communities have included manipulations of AM fungal symbiosis using the fungicide benomyl. The objectives of this study were to evaluate the potential non-target effects of benomyl on soil biota and nutrient cycling in tallgrass prairie and to determine how mycorrhizae may influence these belowground properties. To accomplish these objectives, soil samples were collected during the 1996–1997 growing seasons from long-term benomyl-treated plots established on tallgrass prairie (Manhattan, KS) in 1991, and the following measurements were made: total bacterial and fungal biomass; abundance of nematodes; microbial biomass carbon and nitrogen; substrate-induced respiration; and potentially mineralizable C and N. Long-term benomyl applications resulted in an 80% reduction in mycorrhizal root colonization. By reducing root colonization, benomyl applications resulted in significant decreases in total bacterial biomass and abundance of fungal-feeding and predatory nematodes (20, 12 and 33% reductions compared to control, respectively). Total microbial potential activity (i.e., substrate-induced respiration) increased by 10% with benomyl treatment, whereas the relative contribution of fungi to total microbial activity decreased significantly with benomyl applications. In addition, microbial biomass C increased from 1364 (± 51.2 SE) to 1485 (± 51.2 SE) with benomyl treatment, and total carbon increased significantly (∼8%) only in annually burned soils treated with benomyl. The magnitude of benomyl effects on soil components and processes were small (<33% change with benomyl) relative to effects on mycorrhizal root colonization (80% decrease with benomyl). These results indicate that rather than having large non-target effects, benomyl applications principally affect mycorrhizal root colonization, thereby indirectly influencing soil biota and nutrient availability. Results also indicate that mycorrhizal fungi play an important role in altering the availability and flow of carbon in prairie soil and may influence the composition and abundance of groups of some soil biota. Changes in soil organisms and nutrient availability associated with altered mycorrhizal symbiosis may influence aboveground plant species responses to mycorrhizal suppression, but further research is needed to understand these potential effects.