The transition to zero-net emissions raises trade-offs between the services competing for sustainable carbon sources. Here, we performed a consequential LCA to understand the full environmental performance of managing 1 tonne of wet crop residue to produce sustainable marine fuels, while preserving or enhancing the SOC stocks in French croplands. Three management scenarios were considered: i) decay of crop residues on soils (reference), ii) conversion of crop residues to hydrotreated pyrolysis oil (HPO) to replace heavy fuel oil in maritime transportation, with biochar return to soil, and iii) conversion of crop residues to cryogenic liquefied bio methane (bio-LNG) to replace liquefied natural gas in cargo ships, with digestate return to soil. Besides the replacement of the fossil fuels, a system boundaries expansion was applied to account for the valorisation of the coproducts obtained along the whole supply chain of each system. Results per tonne of crop residues show, for all impacts assessed, a better environmental performance of using crop residues for maritime biofuels in comparison to their direct ploughing to soils, for all environmental impacts assessed. Notably, major GHG savings are observed, representing avoided emissions of 563 and 946 kgCO2etww− 1 of crop residues for the HPO and bio-LNG, respectively. The impact was scaled to the national potential that can be harvested for each pathway without losing SOC stocks (C-neutral harvest), implying a greater potential for the HPO pathway. While bio-LNG was the most performant pathway per tonne of residues (with the exception of marine eutrophication and particulate matter), the scaled results show greater savings with the HPO pathway, except for freshwater eutrophication and water scarcity. The results show that converting crop residues to biofuels while returning the recalcitrant coproduct of the conversion pathway to soils allows, in the HPO case, net environmental benefits for all the assessed environmental impacts as well as for SOC stocks. While bio-LNG shows net savings in most impacts, it shows a net impact for marine eutrophication because of the nitrogen losses associated with the digestate management. Overall, the results do not show, for the assessed pathways and impacts, a trade-off between SOC maintenance and net environmental impacts, if a C-neutral harvest is ensured with the co-product return to soil. This reflects the importance of fossil fuels substitution beyond the sole climate impact.