Intensive tillage, removal or burning of crop residues, limited organic manure use, declining irrigation water resources are the major causes of soil degradation and unsustainability of rice (Oryza sativa L.)-wheat (Triticum aestivum L.) system (RWS) in South Asia. Twelve treatment combinations of green manuring, tillage, and crop residue management included four main plot treatments of wheat straw and Sesbania green manure (GM) management in rice (1) PTRW0, puddled transplanted rice with no wheat straw retained (2) PTRW25, puddled transplanted rice with 25% anchored wheat straw retained (3) PTRW0 + GM, and (4) PTRW25+GM, and three sub-plots treatments (1) CTWR0, conventional tillage wheat with rice residue removed (2) ZTWR0, zero tillage wheat with rice residue removed and (3) ZTWR100, ZTW with 100% rice residue retained as mulch in subsequent wheat. The current study evaluated the effects of wheat straw and green manure practices in rice and tillage and rice straw management on subsequent wheat on changes in soil enzyme (dehydrogenase, fluorescein diacetate, alkaline phosphatase, acid phosphatase, phytase, urease, L-asparaginase, β-glucosidase, xylanase, cellulase, polyphenol oxidase, peroxidase, total polysaccharide carbon, total carbohydrate carbon, total and easily extractable glomalin, microbial biomass carbon and soil respiration) activities and soil chemical properties (pH, electrical conductivity (EC), organic carbon (OC), available N, available P and available K) at different growth stages of wheat after five cycles of continuous RWS. The result showed that PTRW25+GM and ZTWR100 increased wheat yield, chemical properties and soil enzyme activities except polyphenol oxidase and peroxidase. ZTWR100 increased wheat yield by 19.9 and 8.7 % as compared with ZTWR0 and CTWR0, respectively. The majority of the enzyme activities were higher at vigorous vegetative growth stage as compared with the reproductive growth stage. Soil enzyme activities were significantly and positively correlated with each other, OC, available P, available N and grain yield of wheat and negatively correlated with polyphenol oxidase and peroxidase activity. Principal component analysis (PCA) identified dehydrogenase, acid phosphatase, β-glucosidase, microbial biomass carbon and soil respiration as the most sensitive indicators for assessing soil quality for conservation agriculture based RWS. The present study provided reliable biochemical indicators to monitor soil biological quality changes in response to conservation agriculture practices in RWS.