Growing areas under transgenic crops have created a concern over their possible adverse impact on the soil ecosystem. This study evaluated the effect of Bt-cotton based cropping systems on soil microbial and biochemical activities and their functional relationships with active soil carbon pools in Vertisols of central India (Nagpur, Maharastra, during 2012-2013). Culturable groups of soil microflora, enzymatic activities and active pools of soil carbon were measured under different Bt-cotton based cropping systems (e.g., cotton-soybean, cotton-redgram, cotton-wheat, cotton-vegetables and cotton-fallow). Significantly higher counts of soil heterotrophs (5.7-7.9 log cfu g-1 soil), aerobic N-fixer (3.9-5.4 log cfu g-1 soil) and P-solubilizer (2.5-3.0 log cfu g-1 soil) were recorded in Bt-cotton soils. Similarly, soil enzymatic activities, viz. dehydrogenase (16.6-22.67 µg TPF g-1 h-1), alkaline phosphatase (240-253 µg PNP g-1 h-1) and fluorescein diacetate hydrolysis (14.6-18.0 µg fluorescein g-1 h-1), were significantly higher under Bt-cottonsoybean system than other Bt-and non-Bt-cotton based systems in all crop growth stages. The growth stage-wise order of soil microbiological activities were: boll development > harvest > vegetative stage. Significant correlations were observed between microbiological activities and active carbon pools in the rhizosphere soil. The findings indicated no adverse effect of Bt-cotton on soil biological properties.