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Enhancing soil organic carbon (SOC) is an important strategy to sustain and improve the soil quality, mitigate climate change and increase crop productivity under intensive tillage-based rice-wheat (RW) system in the Indo-Gangetic Plains (IGP) of South Asia. Therefore, the effects of tillage, crop establishment, and residue management practices on total as well as different pools of SOC in a sandy loam after 6years of RW system were studied. The imposed three main plot treatments to the rice plots were: (1) ZTDSR, zero till dry seeded rice; (2) CTDSR, conventional till dry seeded rice; and (3) PTR, conventional puddled transplanted rice, and the three sub-plot treatments in succeeding wheat were (i) CTW-R, conventional tillage (CT) wheat with both rice and wheat residues removed; (ii) ZTW-R, zero tillage (ZT) wheat with both the residues removed and (iii) ZTW+R, ZT wheat with rice residue. Total soil organic content increased by 6.5-12.5% and 3.1-12.9% in different soil layers up to 0-60cm depth in ZTDSR followed by ZTW+R over PTR followed by CTW-R practices, respectively. The corresponding increase of the oxidizable C was 4.2-28.2% and 8.2-8.5%, respectively. Significant enhancement in all the carbon pools (non-labile, less labile, labile, very labile pools, water soluble and microbial biomass carbon) and glomalin content were also recorded in ZTW+R treatment. The carbon management index was significantly higher in ZTW+R than ZTW-R and CTW-R treatments. In conservation-based agriculture systems, the principal component analysis revealed that passive pools of SOC and microbial biomass carbon were the most promising and reliable indicators for assessing soil quality. This study showed that adoption of ZTDSR followed by ZTW+R was the better crop production strategy for increasing C-sequestration, improving and sustaining the soil quality and crop productivity in the RW system. This practice also provides an opportunity to retain crop residues as an alternative to burning, which causes severe air pollution in the RW system in the IGP of South Asia.