This article examines the impact of rice–wheat, maize–wheat and cotton–wheat cropping systems on total (TOC), labile and stable organic carbon (C) pools, aggregate stability and distribution of organic C in different size aggregates and the mineral fraction (silt + clay) of soil. The rice–wheat soils had significantly (p < .05) lower TOC concentration (4.46 ± 0.15 g C kg−1) compared with the other two cropping systems. Similarly, water-extractable organic C (WEOC, ∼0.48% of TOC), hot-water-soluble C (HWC, ∼5.5% of TOC) and microbial biomass C (MBC, ∼4.2% of TOC) were significantly lower in soils under rice–wheat compared to the other systems. The formation of water-stable aggregates (WSA) was related to the silt + clay (<0.053 mm) fraction of soils. As the silt + clay fraction increased, the proportion of macro-aggregates (>0.25 mm) increased with a concomitant decrease in the proportion of micro-aggregates (<0.25 mm). The carbon preservation capacity (CPC) of macro-aggregates (CPCMacA), micro-aggregates (CPCMicA) and total water-stable aggregates (CPCWSA) was significantly lower in rice–wheat soils compared with the other systems. The CPCMacA, mineral (silt + clay)-associated C (MinAC) and sodium hypochlorite oxidizable C (NaOCl-C) increased with an increase in the proportion of macro-aggregates and the mineral fraction of soils. A linear increase in the stable C pool ((silt + clay)-C and NaOCl-C) and soils’ silt + clay content implies that soils’ fine fraction was the principal mechanism of textural control on soil organic matter (SOM) stabilization.