Tillage intensive cropping practices have deteriorated soil physical quality and decreased soil organic carbon (SOC) levels in rice–growing areas of South Asia. Consequently, crop productivity has declined over the years demonstrating the need for sustainable alternatives. Given that, a field experiment was conducted for six years to assess the impact of four tillage based crop establishment treatments [puddled transplant rice followed by conventional tillage in wheat/maize (CTTPR–CT), non–puddled transplant rice followed by zero–tillage in wheat/maize (NPTPR–ZT), zero–till transplant rice followed by zero–tillage in wheat/maize (ZTTPR–ZT), zero–tillage direct seeded rice followed by zero–tillage in wheat/maize (ZTDSR–ZT)], two residue management treatments [residue removal, residue retention (~33%)], and two cropping systems [rice–wheat, rice–maize] on soil aggregation, carbon pools, nutrient availability, and crop productivity. After six years of rotation, in top 0.2 m soil depth, zero–till crop establishment treatments (ZTTPR–ZT and ZTDSR–ZT) had higher ( p < 0.05) total organic carbon (TOC) over conventional tillage treatment (CTTPR–CT). Zero–till crop establishment treatments increased very–labile C faction (C frac 1 ) by 21% followed by labile fraction (C frac 2 ) (16%), non–labile fraction (C frac 4 ) (13%) and less–labile fraction (C frac 3 ) (7%). Notably, higher passive C–pool in conservation tillage practices over CTTPR–CT suggests that conservation tillage could stabilize the recalcitrant form of carbon that persists longer in the soil. Meantime, zero–till crop establishment treatments had higher ( p < 0.05) water stable macro–aggregates, macro–aggregates: micro–aggregates ratio and aggregate carbon content over CTTPR–CT. The treatment NPTPR–ZT significantly increased soil quality parameters over CTTPR–CT. However, the effect was not as prominent as that of ZTTPR–ZT and ZTDSR–ZT. Retention of crop residue increased ( p < 0.05) TOC (12%) and soil available nutrients mainly available–P (16%), followed by available–K (12%), DTPA–extractable Zn (11%), and available–S (6%) over residue removal treatment. The constructive changes in soil properties following conservation tillage and crop residue retention led to increased crop productivity over conventional CTTPR–CT. Therefore, conservation tillage (particularly ZTTPR–ZT and ZTDSR–ZT) and crop residue retention could be recommended in tropical rice–based cropping systems for improving soil quality and production sustainability.

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