For three consecutive years Bacillus thuringiensis (Bt) transgenic cotton (var. Mech 162) and its isogenic non Bt counterpart were assessed for the risks of transgenic crop on the soil ecosystem under Indian subtropical conditions. To observe effect of Bt cotton on soil biochemical properties, activities of dehydrogenase, alkaline phosphatase, nitrate reductase and urease soil enzymes were assayed at its different growth stages i.e., seedling, vegetative, flowering, bolling and harvesting stages. To observe effect of Bt cotton on soil microorganisms, number of nematodes, collembola and ants representing micro, meso and macrofauna, respectively were observed in Bt and non- Bt cotton plants rhizosphere at different growth stages. Results showed no significant difference (P&lt;0.05) in alkaline phosphatase, nitrate reductase and urease activity between Bt and non- Bt cotton rhizosphere during crop growth period. However, dehydrogenase activity was significantly high (P&lt;0.05) in the Bt cotton rhizosphere as compared to non Bt cotton rhizosphere throughout the observation period. At most of the growth stages numbers of micro, meso and macro fauna were more in Bt cotton rhizosphere as compared to non Bt cotton rhizosphere. The temporal and spatial variations observed in number of nematodes, collembola and ants between Bt and non Bt cotton plants rhizosphere were significant. The present study shows that the Mech 162 variety of Bt cotton was not posing any risk to soil microorganisms and soil biochemical properties.