Emerging markets for cellulosic bioenergy feedstocks provide opportunities for implementing soil conservation practices that restore soil carbon (C) stocks within agricultural landscapes. Conservation strategies--including conversion to no-till, using cover crops, and establishing perennial vegetation--alter belowground C cycling processes and increase soil C storage through protection of soil organic matter (SOM). In particular, marginal sites less suited for conventionally tilled annual row crops are being targeted as appropriate locations for conversion to perennial bioenergy crops. However, the effects of topography and variations in soil properties on belowground C cycling processes remain largely unknown. The goal of this research is to quantify impacts of variation in topography and edaphic conditions on mechanisms driving short-term (three years) soil C pools under bioenergy crops. I address this goal through studies conducted as part of the Landscape Biomass Project, located in Boone County, IA, using three bioenergy cropping systems (switchgrass, continuous corn, and triticale /sorghum double crop) replicated across five landscape positions along a topographic gradient. Measurement of annual root productivity of cropping systems showed the highest productivity in switchgrass, while continuous corn was the lowest. Annual cropping systems showed no response to topography or soil properties. Switchgrass productivity was lowest on the floodplain and increased with higher soil sand content, suggesting model predictions of root production may be improved by incorporating information on soil texture. Over three years, soil aggregation changes were positive, and were highest under switchgrass. However cropping system effects on aggregation differed between landscape positions. Although total soil C stocks did not change, C physically protected within soil aggregates increased along with unprotected C pools, suggesting that adoption of no-till and conversion to perennial switchgrass increases stored C pools; increases in both pools were greatest under switchgrass. Structural equation modeling of C cycling processes revealed variation in soil properties influenced changes in aggregation and root C inputs, which affected shifts in soil C pools over time. Contrary to previous studies indicating the primary importance of roots and root-associated microbes, these results indicate that soil properties are the main drivers for change in soil C pools over landscapes.