Perennial cropping systems have been proposed as an alternative to conventional, annual cropping systems to improve water quality by increasing nitrogen (N) retention in the plant and soil. In this study, I used a staggered-start experimental design to compare a perennial cropping system, miscanthus (Miscanthus × giganteus Greef et Deu.) at two stand-ages (mature (3 years old), and juvenile (establishment year)) with an annual cropping system, continuous corn (Zea mays L.), across two N fertility treatments of 0 and 224 kg N ha-1. This experiment was duplicated at two locations in Iowa, USA with similar soil parent material, but different background soil fertility due to past fertilizer management. I measured pools and processes associated with N cycling dynamics, including inorganic soil N, net N mineralization, and N leaching. Also measured were soil health indicators, including soil microbial biomass carbon (C) and N, and potentially mineralizable C and N. Measurements were taken at different frequencies over two years. One of the most salient findings in this study was mature miscanthus’ ability to alter soil microclimate properties. Mature miscanthus increased soil temperature by 134% in the winter, and decreased it by 16% during the growing season, compared to continuous corn. Also, during the growing season juvenile miscanthus decreased soil moisture by 10% compared to continuous corn. Across both sites and all treatments net soil N mineralization showed large variability, but the juvenile miscanthus treatment, on average, had the greatest cumulative net N mineralization, and mature miscanthus the lowest. Across all sites and N rates, mature miscanthus reduced nitrate-N leaching by 64% compared to continuous corn. Juvenile miscanthus leached the same amount of nitrate-N as continuous corn. Since miscanthus changed soil microclimate properties and N dynamics compared to continuous corn, it was surprising to find very little effect of miscanthus on soil health indicators – microbial biomass or potentially mineralizable C and N. However, the soil aggregates (< 2 mm diameter) under mature miscanthus could hold 11% more water than that under continuous corn. This study suggests that integrating miscanthus into the Midwestern Corn Belt would substantially reduce N leached through the soil profile, potentially preventing it from being lost to surface or groundwater. Miscanthus shows the potential to provide farm income while reducing the impact of agriculture on water quality, and some signs of improving soil health. More research is needed on the underlying mechanisms driving the differences in soil N dynamics between miscanthus and corn.