Rice–wheat rotations, practised in 12.5 million ha in Indo-Gangetic Plain region (IGPR), are the most important production system for food security of south Asian countries. Recent reports, however, indicate that the system is under production fatigue as yields have started declining due to continuous rice–wheat cultivation. We analysed the yield trends and effect of fertiliser NPK application, alone or in combination with farmyard manure (FYM), green manure (GM) or wheat crop residue (CR) incorporation, on the changes in soil organic carbon (OC) and available NPK contents. Data of a long-term experiment conducted at six locations in the IGPR and at one location in the Central Highlands and Plateau region of India, adjacent to IGPR, revealed that yields of rice and wheat were constantly greater in all the years when complete doses of NPK were applied through fertilisers, or 50% dose of NPK were applied through fertilisers along with organic materials compared to that in unfertilised-control. At Ludhiana and Pantnagar, where yield levels during initial years of the experiment were relatively high, a declining trend in yield was observed over years in all the treatments. At other locations, rice or wheat yield trends in the treatments receiving complete doses of fertiliser NPK were generally not significant, but in the treatments having fertiliser+ manure combination , positive and significant trends in yield of rice were observed. Linear regressions fitted to pooled data across the locations revealed highly significant ( p<0.01) annual increase in yield of rice with integrated supply of nutrients through fertilisers and manures, indicating thereby the advantage of combined use of manures plus fertilisers over fertilisers alone in sustaining crop yields. Soil OC decreased over time at locations where the OC content was greater than 6.5 g kg −1 at the start of the long-term experiment, but increased at locations having initially low (<5.0 g kg –1) OC content. Available P content increased with P additions through fertilisers or manures at four locations. Temporal changes in available P content, however, appeared to have depended on the changes in soil OC. Despite annual K additions at recommended rates through fertilisers and at more than the recommended rates through organic manures, available K content decreased due to continuous cropping at five locations.