Among major cropping systems, rice–wheat system is questioned due to its high contribution in carbon (C) fluxes. To quantify the impact of nutrient management approach on harvestable C-biomass, crop-derived C, soil organic C and N-sequestration, growth, development and yield of rice and wheat, a 2-year field study was executed under conventional tillage (CT) and reduced tillage (RT) in rice-wheat system of Punjab-Pakistan. The fertilization management treatments, including control (T1); treatment 2 (T2, NPK) recommended NPK; treatments 3 (T3, animal manure (M; 20.0 Mg ha-1); treatment 4 (T4, 100% crop residue incorporation; treatment 5 (T5, NPKM5/5) 50% NPK and 50% M; treatment 6 (T6, NPKS5/5) 50% NPK and 50% crop residue; treatment 7 (T7, 0.25NPKM + 0.50S) 25% NPK with 25% M and 50% crop residue and treatment 8 (T8, 0.25NPKS + 0.50M), 25% NPK with 25% crop residue and 50% M were randomly allocated in a split plot design under CT and RT. The results show that organo-mineral treatments (T5-T8) increased harvestable C-biomass by 12.56% and 53.31% relative to the sole organo-mineral (T2-T4) and control (T1) treatments, respectively, under both tillage systems. Further, organo-mineral treatments resulted higher crop-derive C-inputs by 38.27% and 60.72% over control treatment. Additionally, organo-mineral fertilizers significantly reduced the soil bulk density (BD), leading more N-sequestration. The organo-mineral treatments enhanced total dry matter (TDM) of wheat by 30.99 to 53.67%, mean crop growth rate (MCGR) by 30.07 to 65.07%, leaf area index (LAI) by 43.78 to 57.28%, productive tillers by 43.04 to 51.53% and grain yield by 22.52 to 62.31% relative to control under both tillage methods. In rice, organo-mineral treatments enhanced TDM by 35.90 to 54.83%, MCGR by 38.11 to 53.02%, LAI by 21.14 to 51.68% and productive tillers by 11.11 to 32.44% as compared to control. Subsequently, DNDC model successfully captured the trends in SOC contents which is indicated by several statistical indexes such as -0.75 < ME < 0.42, 0.68 g kg−1 < RMSE < 1.06 g kg−1, 0.70 < d < 0.87, 10.94% < nRMSE < 16.26, 4.82 < MPD < 5.77, and 0.31 < MAE < 0.34. In conclusion, an appropriate combination of inorganic NPK, crop stubbles and animal manure could be beneficial to stimulate C-stocks and N-sequestration which directly will alter the soil physical and biological properties for better crop growth and development. Further, DNDC have identified that combine use of inorganic and organic amendments may be beneficial to sequester more SOC sequestration. A greenhouse study was conducted to assess the simultaneous effects of BC and nitrogen (N) fertilization to reduce N2O and CH4 emissions along with higher biomass accumulation in rice under controlled conditions. Nine treatment combinations of BC amendments at 0, 2 and 4% by weight (weight of BC/weight of soil) mixed into 3500 g of unsterile soil with 0, 70 and 140 kg N ha-1 were used in growing rice. Results show that BC-only treatments enhanced the volumetric water contents (VWC) by 9-14% and soil pH by 5-7% coupled with higher daily and cumulative seasonal CH4-C fluxes by 85-95% and 48-51%, respectively, compared with control treatment. Subsequently, the DNDC model also simulated the CH4 emissions trends well in agreement with the measurements. Thus, this study suggests that the use of BC amendment at 2% with 140 kg N ha-1 may be a beneficial strategy to reduce the net GHG emissions from paddy rice in an Alfisol. However, the DNDC model must be calibrated and validated by intensively measurements of additional soil variables including dissolved organic carbon (DOC) and microbial composition after application of different types of biochar.