Understanding the contribution of soil microbes to supporting ecosystem services within agronomic systems is essential for the development of sustainable agronomic systems. This is important as many farmers, in response to the 2007 U.S. Energy Independence and Security Act, are considering growing warm season perennial grasses such as switchgrass (Panicum virgatum) and miscanthus (Miscanthus x giganteus) as cellulosic biofuel feedstock on marginal lands. Perennial cropping systems can support greater local and regional biodiversity and provide more ecosystem services than annual cropping systems. However, management decisions may alter ecosystem services provided by these grassland systems, particularly services influenced by belowground organisms. Our objective for this study was to evaluate the effects of crop identity and fertilization on arbuscular mycorrhizal fungal (AMF) activity and soil nematodes in an ongoing experiment associated with the Great Lakes Biofuels Research Center (GLBRC) and located at the Kellogg Biological Station (KBS) in Michigan, USA. In 2014, we collected soil samples from plots planted in either miscanthus or switchgrass and fertilized at a rate of 72 kg N ha-1 or unfertilized for the previous 5 years. We quantified crop root colonization by AMF, extra-radical mycelium, and plant parasitic nematode abundance in each plot.