This work investigated the effects of land cover and land-use change (LUC) on the ability of a soil to store carbon (C) and reduce carbon dioxide (CO 2) emissions, in a Mediterranean area. Using a paired-site approach, we estimated the effect of land-cover change on the C stock from 1972 to 2008 in a natural reserve (Grotta di Santa Ninfa) in western Sicily. We selected 15 paired sites representative of five LUCs. We studied the effect of land use on soil organic C (SOC) content in bulk soil and in different particle-size fractions (2000–1000 μm, 1000–500 μm, 500–250 μm, 250–63 μm, 63–25 μm, and < 25 μm). Laboratory incubation of the soil samples was conducted to measure CO 2 evolution in bulk soil collected at two different depths from each paired site. We found that the conversion of natural vegetation to orchards (vineyards and olive groves) resulted in SOC decreases ranging from 27% to 50%. The conversion from vineyards to arable land led to a 9% decrease in SOC, whereas the opposite caused a 105% gain. When arable land was replaced by Eucalyptus afforestation, a 40% increase in SOC was observed. SOC decline occurred mainly in coarser soil fractions, whereas the finest fractions were not influenced by land use. We calculated an overall SOC reduction of 63% in the study area, corresponding to a 58 Mg ha − 1 SOC loss in less than 30 years. Our results indicate that land-use conversion, vegetation type, and management practices that control the biogeochemical and physical properties of soil could help reduce CO 2 emissions and sequester SOC. ► The SOC content is strongly affected by land cover and land use change. ► SOC losses are mainly associated with coarser fractions. ► OC content in bulk soil shows a significant negative linear relationship with CO 2 flux.