We analysed results of a long-term experiments, initiated in 1973 on a sandy loam soil under rainfed condition and in 1995–96 on a silty clay loam soil under irrigated condition, to determine the influence of using different combinations of mineral fertiliser (NPK) and fertiliser + farmyard manure (FYM) at 10 Mg/ha on soil organic carbon (SOC) content and its changes in the 0–0.45 m soil depth. Fertilisation always caused a net gain in SOC stock. Such gain was positively proportional to the amount of C incorporated into the soils. Concentration of SOC in the 0–0.45 m depth increased by 44% in NPK + FYM treated plots compared with NPK (44.4 Mg C/ha) after 32 years under rainfed condition and by 14% in the NPK + FYM treated plots compared with NPK (41.76 Mg C/ha) after 9 years under irrigation. Mean (across treatments) total C added under the rainfed and irrigated systems was 2.67 and 3.03 Mg/ha.year, respectively. It was estimated that ~20 and 25% of the gross C input contributed towards the increase in SOC content under the rainfed and irrigated systems, respectively. Carbon loss from native soil organic matter (SOM) averaged ~61 and 261 kg C/ha.year under the rainfed and irrigated systems, respectively. Furthermore, mean stabilisation of added C in the plots under the rainfed condition (~16%) was higher than that (~13%) observed under the irrigated condition. Conversion of total added C to SOC was similar in the NPK and NPK + FYM treated plots under both growing conditions. In the NPK + FYM plots, ~38 and 29% of the C added through FYM was accounted for in the form of total SOC under the rainfed and irrigated conditions, respectively. The estimated quantity of biomass C required to maintain equilibrium SOM content under the rainfed and irrigated systems was 0.29 and 1.08 Mg/ha.year. The total annual C input by the soybean–wheat rotation in the unfertilised control plots under rainfed condition was 0.87 Mg/ha.year and with N fertiliser only under the irrigated condition was 1.75 Mg/ha.year. Thus, SOC augmentation under long-term soybean–wheat cropping was due to higher annual C input than the required amount to maintain equilibrium SOM content. Although FYM addition along with NPK improved total SOC stock and carbon sequestration potential, it did not encourage the stabilisation rate of added C. Hence, C stabilisation that takes into account the total C added in the system is a better indicator of assessing SOC sequestration. In summary, mineral fertilisation improved C sequestration capacity of soybean–wheat system in the Indian Himalayas and manure addition along with mineral fertilisers further improved it.