This study concentrates on developing a soil quality index (SQI), linking productivity to soil quality indicators, and SQI using grain yield of rice and wheat grown in a sequence for 8 years in an integrated tillage-water-nutrient management system. Rice yield was significantly better under puddling, 3 days of drainage, and both 150 % NPK and 100 % NPK + FYM treatments, and the yields were positively correlated with bulk density (BD), available Fe and soil respiration. The wheat yield was significantly higher under conventional tillage, five lots of irrigation, and 150 % NPK, and was positively correlated with BD, water stable aggregates (WSA) and available N. However, it was negatively correlated with mean weight diameter, soil organic carbon and hydraulic conductivity. Stepwise regression identified available Fe, WSA and microbial biomass carbon as the most important indicators that explained 42 % variability in rice yield, which further correlated significantly with the PCA-based SQI (r = +0.44). Thus, crop yield emerged as an important indicator for maintaining soil quality to sustain high productivity under integrated management systems.