2,3 butanediol (BDO) has garnered recent interest due to the high titer concentrations that can be obtained through biochemical routes and its potential for efficient conversion into long-chain hydrocarbons. BDO separation, however, is challenging given its low volatility and high affinity towards water. In this study, two BDO separation pathways were compared, single distillation and combined simulated moving bed (SMB) adsorption with distillation. The separations were incorporated into a 2018 biorefinery design developed by the National Renewable Energy Laboratory (NREL) to produce renewable fuels from corn stover, with BDO as an intermediate and adipic acid as the co-product. The comparison was performed on the basis of sustainability, using lifecycle greenhouse gas (GHG) emissions as the metric. It was found that using a single distillation column gives GHG emissions of 48 gCO2e/MJ for the renewable fuel. This is lower than 93 gCO2e/MJ for petroleum fuel but is higher compared to the SMB-based process which achieves 21 gCO2e/MJ. Additionally, the minimum fuel selling price (MFSP) of each pathway was computed. Single distillation gave a minimum MFSP of $2.54/GGE (gallon of gasoline equivalent) of fuel, while SMB reached $2.45/GGE. The SMB’s MFSP is lower than the Department of Energy’s (DOE) target of $2.50/GGE, demonstrating this pathway is both an economic and sustainable alternative and a sound separation candidate that can enable the viability of the entire biorefinery. The effect of BDO fermentation titer was also considered through a sensitivity analysis.