The last 15 years have seen greatly increased production of corn-based ethanol in the U.S., driven by 2005-2007 mandates to increase renewable fuels production. Perennial bioenergy crops are increasingly important for the production of ethanol and other renewable fuels, however, because they sequester more carbon into the soil and have higher water and nutrient use efficiencies. In this study we consider alternative history scenario in which corn cultivated between 2006–2015 is replaced with second generation perennial bioenergy crops and quantify the impact of this replacement on carbon and energy budget. We hypothesize that perennial bioenergy crops will result in larger carbon uptake and increased soil carbon storage. We first implement corn/soybean rotation in Energy Exascale Earth System (E3SM) Land Model (ELM) and optimize crop parameters using observational datasets. We then simulate corn/soybean production in the US-Midwest during 2006–2015 and study the impact of replacing this production with second generation perennial bioenergy crops.