Changes in direct soil organic carbon (SOC) can have a major impact on overall greenhouse gas (GHG) emissions from biofuels when using life-cycle assessment (LCA). Estimated changes in SOC, when accounted for in an LCA, are typically derived from near-surface soil depths (<30 cm). Changes in subsurface soil depths (>30 cm) could have a large positive or negative impact on overall GHG emissions from biofuels that are not always accounted for. Here, we evaluate how sub-surface SOC changes impact biofuel GHG emissions for corn (Zea mays L.) grain, corn stover, and switchgrass (Panicum virgatum L.) using the (Greenhouse Gases, Regulated Emissions, and Energy Use in the Transportation) GREET model. Biofuel GHG emissions showed as much as a 154% difference between using near-surface SOC stocks changes only or when accounting for both near- and sub-surface SOC stock changes. Differences in GHG emissions highlight the importance of accounting for sub-surface SOC changes especially in bioenergy cropping systems with potential for soil C storage to deeper soil depths. Published by Elsevier Ltd.