The enzymatic activity was evaluated under both Bt and non-Bt systems in varied soil type. The study was conducted during the 2010 wet season (July to December) in a net-house at the Institute of Agricultural Sciences of Banaras Hindu University. It was carried out on three different soil ordersi.e.entisol, inceptisol and alfisol. Bt cotton (cvNCS-138) and its non-transgenic isoline (cvNCS-138) were grown until maturity. A no crop pot was maintained with three replications for all the three soil orders. Study design was a factorial experiment under a completely randomized block design with three replications. The study concludes that soil under Bt cotton cultivar produced significantly higher amount of phosphatase activity than both nonBt and no crop treatments at three growth stages. And the value decreased as the crop growth period advanced. The interaction effect between soil type and Bt-crop was found to be significant in different growth stages throughout the growing season. Results from the study revealed that a significant reduction (9.4%) of the dehydrogenase activity and soil respiration (5%) in the rhizosphere of Bt cotton over non-Bt isoline.