Forests play an important role in the mitigation of global warming, acting as carbon sinks. However, the effects of forest management on the carbon pools over the rotation period in Mediterranean areas are scarcely understood. The objective of this work is to assess the way in which two alternative management systems; one more intensive and the other more moderate (with less severe harvesting and more spread over time) affect the carbon stocks in the living tree biomass, coarse woody debris, forest floor and mineral soil in Mediterranean forests. For this purpose, two chronosequences were established covering the whole rotation period in two Pinus sylvestris L. forests. We conducted four forest inventories over a period of 15 years, measuring the diameter and the height of all the trees higher than 1.3 m in order to calculate the carbon stored in the living parts of the tree. Soil pits were excavated and we collected soil samples to estimate the soil organic carbon. We found that the temporal trends for living tree biomass were similar in both forests. However, the total living tree carbon stored at the end of the rotation period was greater in the forest with the longer rotation period and lighter thinning regime (345.5 Mg ha1 of carbon) than in the intensively-managed forest (223.8 Mg ha1 of carbon). On average, more carbon was found to be stored in the forest floor under the more intensive management system, whereas more carbon was present in the first 20 cm of mineral soil under the moderate management system. Moreover, in each forest, the carbon stocks of the forest floor and in the uppermost cm of the soil remained constant over the rotation period. Therefore, management systems with longer rotation periods and moderate harvesting intensities are recommended to increase carbon fixation in Mediterranean forests.