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In Brazil, studies addressing soil carbon (C) stocks under native vegetation are scarce and often limited to land use change comparisons at the plot level, while studies across larger areas are based on legacy data that address multiple land uses, use wet-oxidations methods to determine C concentrations (Cc) and lack proper soil bulk density (ρb) determinations. Together, these factors may result in either underestimations or biased soil C stocks, thereby hampering the development of adequate land use policy. In this study, we aimed to (i) determine the soil C stocks at different depths (0–10, 10–20, 20–40, 40–60 and 60–100 cm) in Cerrado woodland remnants in Minas Gerais (MG), southeastern Brazil, (ii) study the spatial distribution of soil C stocks using regression-kriging (RK), and (iii) provide a description of the soil C stock distribution and its relationship with variables that drive the soil C stock in the MG Cerrado. We designed a large soil inventory, in which soil samples were collected for soil Cc and ρb determination, to compute soil C stocks in the Cerrado biome of MG. Afterwards, we used RK to model the soil C stocks across the MG Cerrado to a depth of 1 m. Our results show that using RK to map C stocks across different soil layers in the MG Cerrado resulted in accurate estimates. The soil C stocks in the MG Cerrado tend to increase in the west-east direction, are positively correlated with altitude and silt + clay content, and are negatively correlated with the mean annual temperature and total annual precipitation. On average, the C stored at the 0–40 cm layer accounted for 56% of the total C stocked in the top 1 m of soil. Approximately 1.03 Pg of C is stored in the MG Cerrado soils at a depth of 1 m. The average soil C stock in the MG Cerrado is approximately 53% larger than the average indicated for the Brazilian Cerrado. Our results highlight the need for more detailed regional scale soil C inventories in the country to refine national C accounting. We believe our study can aid the development of adequate land use policy and could be used as a baseline for land use change studies in the MG Cerrado.