Crop residues are a key bulk feedstock for supplying renewable carbon for bioenergy production and the broader bioeconomy without compromising food security. However, it is frequently advised to harvest no more than half of this potential to ensure the preservation of soil organic carbon (SOC) stocks. In this study, we challenge this recommendation and demonstrate that the crop residue potential allowing to maintain long-term SOC stocks is spatially differentiated and strongly dependent upon the bioeconomy conversion pathway for which it is intended. We assessed the interaction between the residues' usage for the bioeconomy and the maintenance of SOC stocks over 100 years by considering the coproduct return to soils from five bioeconomy pathways: pyrolysis, gasification, hydrothermal liquefaction, anaerobic digestion, and lignocellulosic ethanol production. To compare the long-term SOC changes from these scenarios against a reference where crop residues are unharvested, we developed a novel framework, applicable to any site or region, by coupling a SOC model that includes recalcitrant organic matter deriving from a bioeconomy calculation module. The adapted SOC model considers the recalcitrance to degradation of each coproduct, while the bioeconomy module determines the share of carbon from the crop residues ending in the coproducts. The framework was tested and applied with a high spatial resolution (>60,000 simulation units) to the context of French croplands over the period of 2020–2120, with state-of-the-art sensitivity analyses. The case study results revealed, among others, that an additional crop residue potential equivalent to 71–225 PJ (pathway-dependent) could be available for the French bioeconomy without SOC decreases, compared to applying a stringent removal limit of 31.5%.