Decline in soil organic carbon (SOC) due to intensive tillage and removal or burning of crop residues is considered a major threat to maintaining soil quality and meeting future challenges of food production at national and global scales. Adoption of conservation-agriculture practices (no till and residue retention) is necessary to promote soil structural stability and increases in SOC content and enzyme activities. We evaluated the impact of tillage and residue-management practices on yield, soil labile-C pools, aggregate stability and soil enzyme activities after seven cycles of a rice (Oryza sativa L.)–wheat (Triticum aestivum L.) system on the Indo-Gangetic Plain of India. Treatments included four combinations of tillage and crop establishment in rice (main plots), and three combinations of tillage and residue management in wheat (subplots). Irrespective of rice-establishment method, mean grain yield of no-till wheat with rice-residue mulch (NTW+RR) was 9% and 22% higher, respectively, than of conventional-till (CTW) or no-till wheat with no rice-residue mulch. Soil C pools (very labile, labile, less-labile and non-labile) were significantly higher under a no-till dry-seeded rice (NTDSR)–NTW+RR cycle than conventional-till puddled transplanted rice–CTW. Macro-aggregates (>0.25 mm) had higher labile C pools, glomalin content and enzyme activities than micro-aggregates. NTW+RR significantly increased soil C pools within both macro- and micro-aggregates. Compared with CTW, NTW+RR increased soil dehydrogenase, cellulase and alkaline phosphatase activities by 23%, 34% and 14%, and water-soluble organic C by 31%, and increased water-stable aggregates and mean-weight-diameter. NTDSR–NTW+RR increased SOC, enzyme activity, aggregate stability and wheat grain yield. Results indicated that soil labile-C pools across aggregate fractions were the most sensitive indicators of soil quality when determining the effects of changes in management practices. Furthermore, adoption of no till and residue retention may improve sustainability in rice–wheat systems of the Indo-Gangetic Plain.