A transformative approach to a more sustainable agriculture has been proposed through developing perennial grain cropping systems, which produce edible grain without the need to till and replant every year. This new type of grain crop has the potential to enhance ecosystem services such as soil C sequestration and nitrogen-use efficiency (NUE). In June 2012, deep soil cores (1m) were taken at the Kellogg Biological Station (KBS) in a field experiment with contrasting cereal crops, an annual winter wheat and a perennial intermediate wheatgrass. The crops were grown under a management gradient (Organic (90 kg N/ha), Low Nitrogen Conventional (90 kg N/ha), and High Nitrogen conventional (120 kg N/ha), providing an opportunity to test interactions of species with management. We quantified above and belowground biomass, root length for both coarse and fine roots, C and N concentrations for all biomass and labile soil carbon in each system. Total root biomass, specific root length (SRL), root diameter, and root surface area (RSA) for both coarse and fine root size fractions were significantly higher in the perennial systems compared to the annual systems (P < 0.05). However, there were no species management-interactions. Overall total plant N content was significantly higher in the perennial system (P<0.05), indicating that from a mass balance standpoint, NUE is greater under perennial systems. Furthermore, greater root N content can result in nutrient recycling for future crop growth. While the labile C fraction (POXC) under the two cropping systems was not significantly different, we found that root C was three times greater than annual systems showing that root C inputs is significantly higher under the perennial system. Our results suggest that the extensive root system of perennial intermediate wheatgrass has the ability to retain nutrients, which is important for C storage and N retention overtime.