To explore the forest harvest effects on biologically active fractions of soil organic matter dynamics, we evaluated soil total carbon (C-total) and soil microbial biomass carbon (SMBC) concentrations, and basal soil respiration (BSR) in old-growth forest (as control) and logged stands (logged one- and 20-yrs ago) in two regions (dry and wet regions) in temperate forests of Oaxaca, Mexico. Mean C-total values were higher in the Dry region than in the Wet region. Greater mean annual precipitation resulted in consistently lower BSR, but had inconsistent effects on the SMBC in dependence upon annual rainfall in the sampling year. In the dry region SMBC was higher in the dry season than in the rainy season, and BSR was higher in soils collected in the rainy season than those collected in the dry season. Forest logging consistently decreased C-total and SMBC concentrations and BSR. In contrast, rainfall seasonality in the Wet region did not affect SMBC concentration or BSR. On the other hand, in this region, the main response to the forest thinning application was an increase in the concentration of C-total. Overall, we conclude that the soil carbon pools and the effects of forest thinning on the biologically active fractions of soil organic matter will vary, depending on the details of the site's annual rainfall amount.