Soil organic matter composition and biochemical properties were determined in mountain calcimorphic Mediterranean soils under different vegetation (cultivated soils, secondary bush, high mountain bush, juniper, evergreen oak and pine) to assess the impact of soil use on the size and activity of microbial communities. Our results indicated that clearing forest leads to a general decline in the performance of soil organic carbon sequestration and associated enzymatic activities. However, when soil enzymatic activities (dehydrogenase, catalase, phosphodiesterase, β-glucosidase, urease and casein-protease) were expressed as ratios to total organic carbon (specific activities), a conspicuous increase in their activities was observed in cleared soils as compared with forest soils, suggesting enhanced hydrolytic potential in the former. In addition, the negative correlation observed between qCO2 (metabolic quotient) and water retention at −1500 kPa, could be interpreted as an adaptive strategy against low soil moisture by microbial communities in cleared soils. This indicates the importance of describing soil quality in terms of long-term soil organic C sequestration and/or resistance of the organic matter to microbial transformation. These features were reflected in the visible and infrared spectra of humic acids, which suggested humification mechanisms involving mainly an alteration of plant macromolecules with poor incorporation of characteristic microbial metabolites in the forest soils whereas the opposite effect was observed in cleared soils.