Long-term sustainability and a declining trend in productivity of rice-wheat rotation in the Indo-Gangetic plain, often direct towards the changes in soil quality parameters. Soil quality is decided through few sensitive soil physical, chemical and biological indicators as it cannot be measured directly. The present investigation was carried out to develop a valid soil quality index through some chosen indicators under long-term influences of tillage, water and nutrient-management practices in a rice-wheat cropping system. The experiment consisted of two tillage treatments, three irrigation treatments, and nine nutrient management treatments for both rice and wheat, was continued for 8 years. The index was developed using expert-opinion based conceptual framework model. After harvest of rice, the CFSQI-P (productivity) was higher under puddled situation, whereas CFSQI-EP (environmental protection) was more under non-puddled condition and 3-days of drainage was found promising for all the indices. No-tillage practice always showed higher soil quality index. The treatments either receiving full organics (100% N) or 25% substitution of fertilizer N with organics showed higher soil quality indices. Puddling, irrigation after 3 days of drainage and substitution of 25% recommended fertilizer N dose with FYM in rice could be practiced for maintaining or enhancing soil quality. No-tillage, two irrigations, and domestic sewage sludge in wheat can safely be recommended for achieving higher soil quality.