Rice-wheat cropping system (RWCS) is the most important system occupying around 26 M ha spread over the Indo Gangetic Plains in South Asia and China. Many long-term trials were led to assess the agronomic productivity and economic profitability of various combinations of conservation agricultural (CA) practices (zero tillage, residue management and crop establishment) in RWCS of Eastern Indo-Gangetic Plains (EIGP) of India. The purpose of this study was to investigate the best management practices involving different tillage-based crop establishment and residue retention techniques and their contribution to agricultural system sustainability through improvement in soil health by developing soil quality index (SQI). We have used SQI as an instrument based on physical [macro aggregate stability (MAS), available water capacity (AWC) and soil penetration resistance (SPR)], chemical [soil organic carbon (OC), available N, available P and available K] and biological [microbial biomass carbon (MBC), fluorescein diacetate (FDA) and dehydrogenase activity (DHA)] properties of soil, because these are very useful indicators of soil’s functions for agronomic productivity and soil fertility. Soil properties like MAS, OC, MBC, FDA and DHA were higher by 47, 18, 56, 48 and 53%, respectively, under ZTDSR-ZTW (T₇: Zero-till direct seeded rice - Zero-till wheat) than RPTR-CTW (T₁: Random puddled transplanted rice - Conventional till broadcasted wheat), at 0-10 cm. CA based treatment T₇ also recorded lower SPR (126 N cm^-1). SQI for different treatments were calculated by performing principal component analysis based on the total data set method. The higher system rice equivalent yield of 12.41 t ha^-1 was observed at SQI value of 0.90 at 0-10 cm and 0.86 at 10-20 cm in T₇. It can be concluded that crop residue retention on the surface with zero tillage is beneficial for the sustainability and productivity of the RWCS in EIGP of India.