Bioenergy cropping systems will supply 16 billion gallons of cellulosic ethanol by the year 2022 in an attempt to reduce U.S. dependence on gasoline. To obtain long-term energy security, bioenergy systems will need to be sustainable, especially with regard to soil. Corn stover, as a bioenergy feedstock, is of great interest due to its immediate availability for harvest with minimal change to current corn-grain cropping systems. However, traditional row crop agriculture of the United States Corn Belt has reduced soil organic matter contents, an indicator of soil quality, by as much as 40 to 60% over the last 150 yr. The harvest of corn stover will directly remove a portion of the soil organic matter input, thus further reducing soil organic matter contents. The reduction in soil organic matter contents produce direct and indirect consequences unfavorable to soil quality and productivity. Therefore, the harvest of corn stover as a long-term bioenergy feedstock is detrimental to soil, impacting soil structure and stability, erodibility, A horizon depth, and physicochemical properties. Perennial biofuel systems, in contrast, have the potential to add soil organic matter to the soil, thus offering long-term enhancement of soil quality, productivity, and formation.