Intensive agriculture has led to generation of a vast volume of agri-residue, prompting a reliance on conservation tillage techniques for prudent management. However, to ascertain the long-term impacts of these practices, the interrelation with the carbon fractions and the biological properties of the soil must be identified. Therefore, in a long-term experiment, five different treatments involving the incorporation of paddy straw as mulch or through disc harrow and farmer practice, including the partial burning of rice straw, were evaluated. After the harvesting of the wheat crop, soil samples collected from 3 different depths (0–15, 15–30 and 30–45 cm) were analyzed for various attributes critical to assessing soil health. Crop residue retention in both seasons (T4) improved carbon fractions, soil microflora viable cell counts and enzyme activities. The principal component analysis (PCA) revealed a positive interaction among the organic carbon, bacterial counts and soil enzyme activities. Thus, a positive impact of conservation tillage techniques involving a minimal disturbance was recorded as improvement in the soil properties, build-up of organic carbon, and wheat productivity in rice–wheat cropping systems.