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The present study aimed to appraise the long-term effects of organics, crop residues, and biofertilisers on soil carbon (C) and nitrogen (N) pools for sustainable crop production and changes in soil quality under long-term organic farming practices. Hence, we studied the soil C and N pools and their sensitivity indices as influenced by a different combination of farmyard manure, vermicompost, biofertilisers, and crop residue of rice, wheat, and mungbean, under long-term rice–wheat–mungbean (RWMCS) and rice–wheat (RWCS) cropping systems in an Inceptisol of India. Total soil organic C increased by 78% and 104% for RWMCS and 94% and 123% for RWCS with FYM + crop residue + biofertilisers and vermicompost + crop residue + biofertilisers, respectively over unfertilised control plots of RWMCS. The highly labile C and microbial biomass C were highly sensitive to management practices compared to total organic C and less labile C fractions. Integrated application of manures and crop residues in FYM + crop residue and VC + crop residue resulted in significantly higher total N, labile N, and mineral N for both cropping systems. Higher values of C and N management indexes were observed with FYM + crop residue + biofertilisers and VC + crop residue + biofertiliser in both cropping systems than other treatments. Integrated use of organic sources had higher N fractions than the unfertilised control plots, indicating that long-term conjoint use of organics, crop residues, and biofertilisers could sustain crop production and soil quality.