Soil organic carbon plays a major role in the global carbon budget, and can act as a source or a sink of atmospheric carbon, whereby it can influence the course of climate change. Changes in soil organic soil stocks (SOCS) are now taken into account in international negotiations regarding climate change. Consequently, developing sampling schemes and models for estimating the spatial distribution of SOCS is a priority. The French soil monitoring network has been established on a 16 km × 16 km grid and the first sampling campaign has recently been completed, providing circa 2200 measurements of stocks of soil organic carbon, obtained through an in situ composite sampling, uniformly distributed over the French territory. We calibrated a boosted regression tree model on the observed stocks, modelling SOCS as a function of other variables such as climatic parameters, vegetation net primary productivity, soil properties and land use. The calibrated model was evaluated through cross-validation and eventually used for estimating SOCS for the whole of metropolitan France. Two other models were calibrated on forest and agricultural soils separately, in order to assess more precisely the influence of pedo-climatic variables on soil organic carbon for such soils. The boosted regression tree model showed good predictive ability, and enabled quantification of relationships between SOCS and pedo-climatic variables (plus their interactions) over the French territory. These relationship strongly depended on the land use, and more specifically differed between forest soils and cultivated soil. The total estimate of SOCS in France was 3.260 ± 0.872 PgC for the first 30 cm. It was compared to another estimate, based on the previously published European soil organic carbon and bulk density maps, of 5.303 PgC. We demonstrate that the present estimate might better represent the actual SOCS distributions of France, and consequently that the previously published approach at the European level greatly overestimates SOCS.