Managing soil carbon requires accurate estimates of soil organic carbon (SOC) stocks and its dynamics, at scales able to capture the influence of local factors on the carbon pool. This paper develops a spatially explicit methodology to quantify SOC stocks in two contrasting regions of Southern Spain: Sierra Norte de Sevilla (SN) and Cabo de Gata (CG). Also, it examines the relationship between SOC stocks and local environmental factors. Results showed that mean SOC stocks were 4·3 kg m−2 in SN and 3·0 kg m−2 in CG. Differences in SOC in both sites were not significant, suggesting that factors other than climate have a greater influence on SOC stocks. A correlation matrix revealed that SOC has the highest positive correlation with clay content and soil depth. Based on the land use, the largest SOC stocks were found in grassland soils (4·4 kg m−2 in CG and 5·0 kg m−2 in SN) and extensive crops (3·0 kg m−2 in CG and 5·0 kg m−2 in SN), and the smallest under shrubs (2·8 kg m−2 in CG and 3·2 kg m−2 in SN) and forests soils (4·2 kg m−2 in SN). This SOC distribution is explained by the greatest soil depth under agricultural land uses, a common situation across the Mediterranean, where the deepest soils have been cultivated and natural vegetation mostly remains along the marginal sites. Accordingly, strategies to manage SOC stocks in southern Spain will have to acknowledge its high pedodiversity and long history of land use, refusing the adoption of standard global strategies. Copyright © 2015 John Wiley & Sons, Ltd.