Monitoring and estimating spatially resolved changes in soil organic carbon (SOC) stocks are necessary for supporting national and international policies aimed at assisting land degradation neutrality and climate change mitigation, improving soil fertility and food production, maintaining water quality, and enhancing renewable energy and ecosystem services. In this work, we report on the development and application of a data-driven, quantile regression machine learning model to estimate and predict annual SOC stocks at plow depth under the variability of climate. The model enables the analysis of SOC content levels and respective probabilities of their occurrence as a function of exogenous parameters such as monthly temperature and precipitation and endogenous, decision-dependent parameters, which can be altered by land use practices. The estimated quantiles and their trends indicate the uncertainty ranges and the respective likelihoods of plausible SOC content. The model can be used as a reduced-form scenario generator of stochastic SOC scenarios. It can be integrated as a submodel in Integrated Assessment models with detailed land use sectors such as GLOBIOM to analyze costs and find optimal land management practices to sequester SOC and fulfill food–water–energy–-environmental NEXUS security goals.