Due to climate change and energy security concerns, bioenergy products and systems are becoming increasingly important, and Life Cycle Assessment (LCA) can provide a better understanding of their carbon efficiency. In this study, we used a cradle-to-grave LCA to analyze the carbon efficiency of a cottonwood-switchgrass agroforest system grown on agriculturally marginal soils on three sites established in 2009 in the Lower Mississippi Alluvial Valley (LMAV). A complete carbon inventory was done for both the agroforestry bioenergy system and a control cropping system that rotated soybeans and grain sorghum. Three years after establishment, the cottonwood sequestered the highest amount of carbon in dead roots, live roots, and surface residues (3222 kg ha−1) and the switchgrass sequestered the highest amount of carbon in above-ground biomass (4233 kg ha−1). The maximum carbon was emitted (1733 kg ha−1) from the soybean/grain sorghum rotation production system. The carbon emission during production was not statistically different for the bioenergy crops. Carbon emission from both bioenergy crops were significantly different compared to traditional agricultural crops. At the end of the third growing season, cottonwood showed the best performance in the net (6.2) and gross (11.8) ratios of carbon balance. The gross ratio of carbon by switchgrass (11.6) was comparable to cottonwood, but the net ratio was approximately 50% (3.3). The net and gross ratios of carbon balance were positive for the control cropping system as well, 1.2 and 2.2 respectively. Carbon emission from the traditional agricultural production system was at least 234% higher compared to the dedicated bioenergy production system. It was evident that bioenergy crops provide a more environmentally efficient practice in terms of carbon balance than the traditional agricultural practice in the Lower Mississippi alluvial Valley.