The utilization of crop residues in the production of second-generation biofuels has the potential to boost the bioenergy sector without affecting food commodity prices. However, policies leading to large-scale biomass removal should carefully balance the consequences, both environmental and in terms of emissions, on soil organic carbon (SOC) stocks depletion. Using a recently developed simulation platform, SOC changes were estimated at European level (EU + candidate and potential candidate countries) under two scenarios of low (R30) and high (R90) maize stover removal for cellulosic ethanol production (i.e. 30 and 90 % of stover removal, respectively). Additionally, mitigation practices for SOC preservation, namely the introduction of a ryegrass cover crop (R90_C) and biodigestate return to soil (R90_B), were explored under the highest rate of stover removal. The results showed that 15.3 to 50.6 Mt year−1 of stover (dry matter) would be potentially available for ethanol production under the lower and high removal rates considered. However, large-scale exploitation of maize residues will lead to a SOC depletion corresponding to 39.7–135.4 Mt CO2 eq. by 2020 (under R30 and R90, respectively) with greater losses in the long term. In particular, every tonne of C residue converted to bioethanol was predicted to have an additional impact on SOC loss almost ranging from 0.2 to 0.5 CO2 eq. ha−1 year−1, considering a continuous biofuel scenario by 2050. The mitigation practices evaluated could more than halve SOC losses compared to R90, but not totally offsetting the negative soil C balance. There is a pressing need to design policies at EU level for optimum maize biofuel cultivations that will preserve the current SOC stock or even generate C credits.