We compare the life cycle greenhouse gas (GHG) emissions of converting corn stover to ethanol using a stochastic life cycle model that accounts for model variable uncertainty in feedstock production and fuel conversion. Life cycle GHG emissions per unit of land (ha) may vary by region due to soil differences, existing land uses, and ethanol yield. We develop scenarios that investigate how cover crop planting and the decision to convert residual (carbon-rich) lignin and solids separated following feedstock pretreatment to electricity or to reapply it on agricultural land in order to restore SOC and thus remove large fractions (up to 70%) of stover for conversion to ethanol, which would displace greater quantities of gasoline, change life cycle GHG emissions significantly. Because of lignin’s slow decomposition, the carbon fraction of this component of lignocellulose should remain undigested in soils for longer periods than if fractions of stover complete with cellulose, hemicellulose, and lignin, were left on the land. Given the uncertainty of today’s conversion technology, and variability in ethanol yield, converting residual lignin to electricity avoids releasing more GHGs (3.5±0.9 g CO2 eq./ha/year) than does returning lignin to agricultural land (2.2±0.6 g CO2 eq./ha/year). With anticipated improvements in ethanol yield through pilot scale testing, the balance of avoided GHG emissions could shift in favor of land application of lignin due to greater displacement of gasoline fuel. We hypothesize that under both scenarios, cover crop planting enhances gasoline displacement thereby allowing for greater net displacement of GHG emissions and additionally improves SOC.