Crop residues are key to supply carbon to the bioeconomy without interfering with food security. However, it is often suggested to export no more than half of this potential to ensure the maintenance of soil organic carbon (SOC) stocks. In this study, we challenge this idea by assessing how the residues use for the bioeconomy is intertwined with the maintenance of long-term SOC stocks, and thus the amount that can safely be harvested. We considered the coproduct return to the soil from five bioeconomy scenarios: i) pyrolysis biochar, ii) gasification biochar, iii) hydrothermal liquefaction hydrochar, iv) anaerobic digestion digestate, and v) lignocellulosic ethanol molasses. To compare the long-term SOC changes from these scenarios against a business-as-usual (BAU) scenario, in which crop residues are left unharvested, we developed an original framework coupling a SOC model with a bioeconomy module, that we applied at high spatial resolution to cover over 60,000 combinations of crop rotations and pedoclimatic units over France, for 2020–2120. The SOC model was adapted to consider the recalcitrance to degradation of each coproduct, while the bioeconomy module determines the share of carbon from the crop residues allocated to the coproducts. Our results show that crop residues could be completely harvested if biochar from pyrolysis or gasification is returned to soils, with SOC expected to double as compared to the BAU scenario. Replacing crop residues with hydrochar was shown to increase SOC stocks in 87% of the areas (max + 8%), while the digestate scenario predicted minor SOC increases in 50% of the areas (max + 0.76%) and decreases in 40% of the areas (min − 4%). The molasses scenario yielded SOC losses in all the areas and is thus not recommended as a C maintenance strategy. Excluding these, an additional amount of 60.4–191 PJ of crop residues (use-dependent) could be available for the French bioeconomy in comparison to applying a universal removal rate of 31.5%.