Forest expansion in Mediterranean mountain areas is a widespread phenomenon resulting from the abandonment of agricultural and pastoral activities during the last century. Therefore, knowledge of the long-term storage capacity of soil organic carbon (SOC) in Mediterranean forests is of great interest in the context of global change. However, the effects of these land uses and covers (natural secondary forest, afforestation with conifers and silvo-pastoral ecosystems (dehesas)) on SOC dynamics are still uncertain. The main objectives of this study were to evaluate physico-chemical soil properties, SOC and nitrogen stocks, and SOC fractions in Mediterranean forests and to assess the effects of tree species, the soil environment (acidic and alkaline), and land management. We selected five land uses and land covers: managed and non-managed afforestation and dehesa (except for alkaline dehesa) and a stage of succession when tree species begin to become established after abandonment. This study concludes that although total SOC stocks are higher in afforested systems with conifers, SOC is stored in less stable carbon pools than in broadleaf forests. In addition, this study confirms that there are marked differences in the results between acidic and alkaline environments. Finally, the management system is also a significant factor, particularly for afforested sites.