Technical Abstract: Background/Question/Methods Corn stover has been suggested as a viable biomass feedstock for bioenergy production. However, unharvested corn stover provides two important ecosystem services: it reduces soil erosion and replenishes soil carbon, both of which help maintain soil productivity. There are several strategies which could help maintain these services. To mitigate soil erosion, 1) the amount of corn stover harvested could be constrained so the quantity needed to mitigate soil erosion is met or 2) a winter cover crop could be planted to protect the soil from erosion losses. To mitigate for soil carbon losses 1) corn stover harvest could be constrained so soil carbon needs are met, 2) a cover crop could be planted to substitute for carbon removed with corn stover, or 3) a high lignin residue can be separated from the cellulose/hemicelluloses fractions in the biorefinery and then land applied. We used the biogeochemical model DAYCENT to quantify the changes in soil carbon with each of these scenarios and their impact on soil N2O emissions across the Corn Belt. We then compare the net life cycle greenhouse gas (GHG) emissions of each strategy by coupling DAYCENT and farm operations with a biorefinery model. Results/Conclusions Soil carbon decreased for some locations when corn stover was removed. Locations with higher corn grain and stover yields could withstand higher corn stover harvests while maintaining biomass inputs for sustaining soil carbon. Rye biomass carbon inputs could mitigate for removal of carbon from corn stover. With reduced soil nitrate losses, indirect soil N2O losses were lower. However, when the rye winter cover crop was fertilized to increase potential yields for use as a biomass feedstock rather than for mitigation of soil carbon and nitrate losses, nitrate losses increased and consequently indirect N2O losses increased. When high lignin residue from the biorefinery was returned and applied to the field, these carbon inputs mitigated the soil carbon losses from corn stover removal. The recently recognized need to maintain soil carbon in addition to protecting from soil erosion losses limits the near term potential of corn stover as a bioenergy feedstock. However, with future increases in corn yield, greater amounts of corn stover could potentially be harvested while maintaining soil carbon. Although winter cover crops have great potential for reducing the environmental impacts of corn production, the inability to monetize these benefits and provide a return to the farmer for the costs incurred have limited the adoption of this practice to those areas receiving government subsidy.