Bioenergy production could provide more sustainable energy and reduce dependency on fossil fuels, while using existing infrastructure for fuel delivery. Crop stover, not used for food, represents an important feedstock for biofuel production, but its removal could lead to lower soil carbon stocks. This study examines the relative contributions of cover crop root and shoot to soil carbon in order to determine whether belowground cover crop carbon could help offset the deleterious effects of residue removal in a no-till continuous corn bioenergy cropping system.