A field experiment was conducted to investigate the influence of long-term application of organic manures on aggregate stability, associated carbon concentrations and carbon pools as an important soil-quality parameter under a scented rice-potato-onion cropping system in silt-loam textured soil in Eastern Bihar, India (subtropical climatic condition). Five treatments were used: 1) nitrogen, phosphorus and potassium (NPK) - 100% recommended dose of NPK; 2) NPK+FYM (farmyard manure) - 50% NPK+50% N as FYM; 3) FYM+VC (vermicompost)+ NC (neem cake) - different organic sources each equivalent to 1/3 of the recommended N (FYM +VC +NC); 4) FYM+VC+NC+PSB (phosphate-solubilizing bacteria - different organic sources each equivalent to 1/3 of the recommended N (FYM +VC+NC)+biofertilizers containing N and P carriers (PSB) and 5) FYM+BFN +BM+PSB - 50% N as FYM +biofertilizer for N +Bone meal to substitute P requirement of crops +PSB. The aggregate size distribution (> 250 mu m) at different soil depths is higher in treatment FYM+VC+NC+PSB and is at par with FYM+VC+NC, followed by FYM+BFN+BM+PSB and NPK+FYM, and the lowest in treatment receiving 100% NPK. The mean carbon concentration in each soil fraction was higher in soil depth 0-10 cm, followed by 10-20 cm and 20-30 cm. The trend of mean weight diameter (MWD) in different treatments was FYM+VC +NC+PSB >= FYM+VC+NC > NPK+FYM > FYM+BFN+BM+PSB > NPK. The trend of carbon concentrations in different treatments was FYM+VC+NC+PSB >= FYM+VC +NC > FYM+BFN+BM+PSB >= NPK+FYM > NPK. Non-labile pool of carbon forms the major portion (60.14%) of the total soil organic carbon (SOC) irrespective of all depths. Bulk density (BD) has a significant role in stabilizing soil aggregates as well as increasing the SOC content in soil. SOC was negatively correlated with BD (r = -0.870, p = 0.05), MWD (r = -0.911, p = 0.01) and geometric mean diameter (GMD) (r = -0.958, p = 0.05) irrespective of depth. This study took further steps toward understanding the enhancing of aggregate stability on organic manures addition for soil quality improvement.