The aim of this study was to evaluate microbial activity in soils under conventional and organic agricultural system management regimes. Soil samples were collected from plots under conventional management (CNV), organic management (ORG) and native vegetation (AVN). Soil microbial activity and biomass was significantly greater in ORG compared with CNV. Soil bulk density decreased three years after adoption of organic system. Soil organic carbon (SOC) was higher in the ORG than in the CNV. The soil under organic agricultural system presents higher microbial activity and biomass and lower bulk density than the conventional agricultural system.