Energy cover crops for biogas production through anaerobic digestion (AD) are inserted between two primary crops. They replace either bare soil or non-harvested cover crops, and their management is usually intensified to produce more biomass. They allow the production of renewable energy as well as diges-tate, used as an organic fertilizer, without directly competing with food produc-tion. Because of the increased biomass production and export and of the return of a digested biomass to the soil, the impact of energy cover crops on soil organic carbon (SOC) is questioned. The objective of this paper was to study the differ-ence in SOC stocks induced by the introduction of energy cover crops for AD coupled with the application of the resulting amount of digestate. We used the AD model Sys- Metha combined with the soil C model AMG to simulate SOC stocks for 13 case studies in France, with scenarios comparing different inter-crop management practices, with or without cover crops, harvested or not. Our results indicated that the higher biomass production of energy cover crops (from 6.7 to 11.1 t DM ha−1) in comparison with nonharvested cover crops (2 t DM ha−1) or bare soil led to higher humified C input (belowground input and digestate), despite the high C fraction exported in AD. This resulted in an increase in SOC stocks in comparison with nonharvested cover crops or bare soil (from 0.01 to 0.12 t C ha−1 year−1 over 30 years). The uncertainties in the model parameters did not modify these results. However, in the case of equal biomass production be-tween energy cover crops and nonharvested cover crops, SOC stocks would be lower with energy cover crops.