The objective of this study was to evaluate the effects of conventional (inorganic) and organic agricultural systems on the physico chemical and microbial properties of soil. Microbial population counts were analyzed from soil samples collected from the surface (0-10 cm) and sub surface (10-20 cm) soil depths of the treated plots by soil plate and dilution plate methods for bacteria. Results of the physico chemical analysis showed that the inorganically treated plots had significantly higher pH, nitrogen, potassium, phosphorus contents than the organically treated plots. On the other hand organically treated plots have the maximum microbial population counts and microbial biomass carbon which is followed by the inorganically treated plots and control. Organic plots exhibited a significant variation in bacterial population in both the soil depths with the inorganically treated plots and control. The application of organic fertilizers increased the organic carbon content of the soil and thereby increasing the microbial counts and microbial biomass carbon. The use of inorganic fertilizers resulted in low organic carbon content, microbial counts and microbial biomass carbon of the soil, although it increased the soil’s nitrogen, phosphorus and potassium level which could be explained by the rates of fertilizers being applied. From the present study it has been concluded that the soil under organic agricultural system presents higher microbial activity and microbial biomass carbon than the conventional or inorganic agricultural system.