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Background Benefits to agricultural yield improvement, soil degradation prevention, and climate mitigation are central to the synergies of soil organic carbon (SOC) build-up. However, the contributions of small-scale farmers, the main target of recent agricultural and rural development policies, to SOC enhancement are understudied. Here, we present a global analysis of small-scale farmers’ contributions to the potential of additional SOC stocks and the associated increase in crop production. Methods We applied random forest machine learning models to global gridded datasets on crop yield (wheat, maize, rice, soybean, sorghum and millet), soil, climate and agronomic management practices from the 2000s (n = 1808 to 8123). Using the established crop-specific SOC-yield relationships, the potentials of additional SOC build-up and crop production increase were simulated. The estimated SOC increase was converted into global decadal mean temperature change using the temperature sensitivity to cumulative total anthropogenic CO2 emissions from preindustrial levels. The amount of inorganic nitrogen (N) input that would result in the same yield outcome as the SOC build-up was derived from the crop-specific N-yield relationships. Results SOC contributes to yields in addition to management and climatic factors. Additional SOC sums up to 12.78 GtC (11.55–14.05 GtC) of global SOC stock, which earns 38.24 Mt (22.88–57.48 Mt) of additional crop production and prevents warming by 0.030 °C (0.019–0.041 °C). This production increase equates to what would be achieved by an inorganic N input of 5.82 Mt N (3.89–7.14 Mt N). Small-scale farmers account for 28% (26–30%) of the additional SOC build-up and 17% (15–20%) of the production increase. Key crops and regions in terms of small-scale farmers’ contributions include Sub-Saharan African maize and rice, Latin American and Caribbean soybean and maize, and South Asian rice and wheat. Conclusions The contribution of small-scale farmers to the potential increase in SOC stock and crop production is sizable, which in theory further leads to saving inorganic N input. These findings emphasize the importance of linking soil management to sustainable land and climate mitigation with institutions and policy for small-scale farmers. Such a joint policy would assist multiple development goals.