Key soil parameters, organic matter, soil pH and plant nutrients determine the capacity of a soil to sustain plant and animal productivity. Conservation agriculture (CA) and crop diversification or intensification may change these soil parameters positively or negatively, which eventually affect long-term sustainability. We monitored these key soil properties (at depths of 0–15 and 15–30 cm) under CA-based sustainable intensification practices: zero-till (ZT), and crop residue retention, and crop rotations on Inceptisols and Entisols in the Eastern Ganga Alluvial Plains from 2014 to 2017. The rainfall of this sub-tropical region is 1273–3201 mm. Soil organic carbon (C) ranged within 0.46–1.13% and generally followed (positive) rainfall gradients. At all sites, the soil under ZT tended to have higher organic C than conventional tillage (CT). Soil pHH2O ranged within 5.7–7.8 across the region. At all sites, soil pH generally decreased under ZT compared to CT. This was most marked at some acidic soil sites where pH decreased by up to 0.4 units; the lower the initial soil pH, the higher was the decrease in pH under ZT practice. In contrast, the reverse trend was observed for soil organic C. Partial nutrient balances for N, P and K in rice–wheat and rice–maize systems were positive for N and P (<50 kg ha–1) but negative for K (up to 90 kg ha–1) under both tillage practices; more so under ZT practice even though crop residues were retained. Changes under ZT provide an opportunity to maintain soil organic C. However, remediation measures such as liming and efficient use of fertilisers are required for long-term sustainability of the farming systems in this agriculturally important region of South Asia.