Conversion of corn (Zea mays L.) stover to biofuel is among the portfolio of potential options to reduce over-dependence on fossil fuels and net CO₂ emissions. The extent to which the stover removal for biofuel production affects the soil organic carbon (SOC) storage and CO₂ fluxes in no-till systems is not well documented. We quantified the total SOC and CO₂ fluxes from three soils managed with varying quantities of stover under no-till corn after one year of stover management in Ohio. The three soils were: Rayne silt loam (RSL), Hoytville clay loam (HCL), and Celina silt loam (CSL), each comprising six treatments of 0 (T0), 25 (T25), 50 (T50), 75 (T75), 100 (T100), and 200 (T200) % of corn stover corresponding to 0, 1.25, 2.50, 3.75, 5.00, and 10.00 Mg ha^-1 of stover, respectively. Stover harvesting had a rapid and significant effect on total SOC and CO₂ fluxes, but the effects were soil-dependent. Mass SOC in the 0- to 5-cm soil depth decreased with increasing stover removal at all but HCL (P<0.01). Complete stover removal reduced mass SOC (19.0 vs. 13.7 Mg ha^-1) by 39% for the RSL and by (21.0 vs. 15.4 Mg ha^-1) 30% for the CSL compared to T100, indicating that SOC changes were positive (gains) when stover is returned and negative (losses) when stover is removed. The CO₂ fluxes increased with increasing rates of stover retention for the RSL where fluxes from T0 were 87% and 73% of those from T75 and T100, respectively. Significant CO₂ losses from mulched soils may, however, be offset by the increased SOC storage. Results show that stover removal effects on SOC and CO₂ fluxes can be rapid, but further research is needed to determine the long-term stover removal-induced changes in SOC storage.