A thorough knowledge of the effects of climate and land use changes on the soil carbon pool is critical to planning effective strategies for adaptation and mitigation in future scenarios of global climate and land use change. In this study, we used CarboSOIL model to predict changes in soil organic carbon stocks in a semi-natural area of Southern Spain in three different time horizons (2040, 2070, 2100), considering two general circulation models (BCM2 and ECHAM5) and three IPCC scenarios (A1b, A2, B2). The effects of potential land use changes from natural vegetation (Mediterranean evergreen oak woodland) to agricultural land (olive grove and cereal) on soil organic carbon stocks were also evaluated. Predicted values of SOC contents correlated well those measured (R2 ranging from 0.71 at 0–25 cm to 0.97 at 50–75 cm) showing the efficiency of the model. Results showed substantial differences among time horizons, climate and land use scenarios and soil depth with larger decreases of soil organic carbon stocks in the long term (2100 time horizon) and particularly in olive groves. The combination of climate and land use scenarios (in particular conversion from current ‘dehesa’ to olive groves) resulted in yet higher losses of soil organic carbon stocks, e.g. − 30, − 15 and − 33% in the 0–25, 25–50 and 50–75 cm sections respectively. This study shows the importance of soil organic carbon stocks assessment under both climate and land use scenarios at different soil sections and point towards possible directions for appropriate land use management in Mediterranean semi natural areas.