Management of enormous amounts of crop residues generated from increased crop productivities is a serious issue and could be dealt with by composting. Understanding the effects of such compost application on soil carbon (C) and nitrogen (N) cycles is important for assessing acceptable organic sources for a particular region. We appraised the sensitivity indices and C and N pools in soils amended with full and 50% substitution of mineral fertilisers with rock phosphate enriched composts prepared from rice straw, mustard stover and tree leaves under a four-year-old wheat (Triticum aestivum)–green gram (Vigna radiata) cropping sequence in an Inceptisol. Results revealed that total organic C (TOC) increased by ~37 and 49% under tree leaf compost and tree leaf compost + 50% NPK-treated plots respectively, over unfertilised control in wheat. However, the corresponding increases were ~33 and 36% over control for green gram. The very labile C pool was more sensitive to management than TOC and less labile C. After wheat, significant improvements in total N, labile N and mineral N were found in plots receiving enriched composts applied either alone or in combination with 50% NPK. The carbon management index (CMI), nitrogen management index (NMI) and microbial C : N ratio were similar in soils amended with rice straw compost + 50% NPK, mustard stover compost + 50% NPK and tree leaves compost + 50% NPK, indicating suitability of all three organic sources in this zone. The highest values of CMI (219) and NMI (274) were maintained in mustard stover compost + 50% NPK and rice straw compost + 50% NPK-treated plots respectively. All enriched composts + 50% NPK plots had sensitivity indices (of different C and N pools) either nearer to or higher than 100% NPK plots, implying that the present integrated nutrient management with enriched composts + 50% NPK could sustain crop production and thus could be recommended.