Clay–organic complexes (COC) impart chemical and physical protection to soil carbon (C). In the present study, the aim was to assess the long-term effects of different organic amendments on C stability in COC, distribution of the aggregates, C concentration in the aggregates and labile organic C fractions in the inceptisols located at the research farm situated in the semi-arid sub-tropical climate of India. The results showed that the COC, the percentage of large macroaggregates (LMA) (>2 mm) and the C associated with the aggregates decreased through the soil depths, whereas the other size fractions of soil aggregates (<2 mm) showed an increasing trend. The COC was significantly higher (4.4 times) in soil treatments where farmyard manures (FYM), green manure (GM) and biofertilizers (BF) were applied together (FYM + GM + BF). The organic amendments increased the proportion of LMA over control (no application of organic amendments) to a magnitude of 83 to 101% and the C associated with LMA to a magnitude of 0.48 to 9.8% over control in surface soil. On average, the combined application of FYM, GM and BF exhibited higher C accumulation in almost all soil aggregate fractions, except microaggregates (mA), i.e., (0.25–0.053 mm) size fractions, where application of FYM alone recorded the highest value. Averaged over soil depths, the particulate organic C (POC), dissolved organic C (DOC) and potassium permanganate oxidizable C (POXC) were significantly higher under integrated organic treatments than individual amendments. The significantly higher correlation between COC and the percentage of LMA and aggregate-associated C implied their direct role in soil aggregate formation and their stability. The carbon stability, i.e., retention time of humus in soil, was significantly correlated with soil organic carbon, dissolved organic carbon, particulate organic carbon, potassium permanganate oxidizable C, C mineralization (Cmin), glomalin-related soil protein (GRSP), macroaggregate (MA)-associated C and rice equivalent yield (REY). Overall, the data suggest that the combined application of FYM + GM + BF promotes soil quality under rice–wheat rotation in inceptisols in semi-arid sub-tropical India.