Biofuel feedstock systems could impact Midwestern USA marginal soils by altering soil organic carbon (SOC) pools, with the potential for increased carbon sequestration. Land-use conversion of marginal land from managed perennial grazing land to annual and perennial biofuel feedstocks may result in an immediate loss of SOC through accompanying tillage, but little is known regarding the potential for long-term (< 5 years) SOC stabilization and positive sequestration, especially across diverse bioenergy crops. Therefore, an eight-year study was conducted (est. 2010) to quantify the effects of converting forage systems on marginal land to annual and perennial bioenergy crop production on SOC pools in central Missouri, USA. Three groups were selected: (1) annual grass crops, consisting of sweet sorghum (Sorghum bicolor (L.) Moench) and high biomass sorghum (HBS), (2) perennial grass crops, consisting of two biotypes of switchgrass (Panicum virgatum), and (3) two short-rotation tree crops, willow (Salix spp.) and eastern cottonwood (Populus deltoides). These crops were selected for their well-documented rapid and high above-ground biomass accumulation and potential for energy conversion. Soil samples were collected in the first and eighth years from to a soil depth of 60 cm then analyzed for concentrations of SOC and active carbon (AC) pools and stocks calculated to evaluate any real differences in carbon sequestration among the diverse bioenergy crops. The below-ground effects of the carbon additions by the dynamic root systems of the several measured crops in the study could result in SOC pool stabilization and potential for increased carbon sequestration, even as land-use conversion may result in early soil carbon losses.