Gaseous streams in biorefineries have been undervalued and underutilized. In cellulosic biorefineries, coproduced biogas is assumed to be combusted alongside lignin to generate process heat and electricity. Biogas can instead be upgraded to compressed biomethane and used as a transportation fuel. Capturing CO2-rich streams generated in biorefineries can also contribute to greenhouse gas (GHG) mitigation goals. We explore the economic and life-cycle GHG impacts of biogas upgrading and CO2 capture and storage (CCS) at ionic liquid-based cellulosic ethanol biorefineries using biomass sorghum. Without policy incentives, biorefineries with biogas upgrading systems can achieve a comparable minimum ethanol selling price (MESP) and reduced GHG footprint ($1.38/liter gasoline equivalent (LGE) and 12.9 gCO2e/MJ) relative to facilities that combust biogas onsite ($1.34/LGE and 24.3 gCO2e/MJ). Incorporating renewable identification number (RIN) values advantages facilities that upgrade biogas relative to other options (MESP of $0.72/LGE). Incorporating CCS increases the MESP but dramatically decreases the GHG footprint (−21.3 gCO2e/MJ for partial, −110.7 gCO2e/MJ for full CCS). The addition of CCS also decreases the cost of carbon mitigation to as low as $52–$78/t CO2, depending on the assumed fuel selling price, and is the lowest-cost option if both RIN and California’s Low Carbon Fuel Standard credits are incorporated.