AbstractCorn stover is expected to supply much of the cellulosic biomass required to meet the 61 billion liters per year target under the US Energy Independence and Security Act. The Act also requires that cellulosic biofuels achieve a greenhouse gas (GHG) reduction of 60% compared to gasoline. If corn stover is harvested for biofuels, it can no longer help replenish soil organic matter, and net soil carbon emissions increase. So meeting the GHG reduction target is a concern. We studied the effect of stover removal on overall GHG emissions of corn stover ethanol systems in the 12‐state Corn Belt region. Even at a stover removal rate of 66%, no more than 20 billion liters can be annually produced while simultaneously satisfying the 60% GHG reduction. Moreover, no GHG reduction relative to gasoline occurs in short time periods. The GHG benefits of corn stover ethanol only appear after longer time periods. © 2017 Society of Chemical Industry and John Wiley & Sons, Ltd