A long-term fertilizer experiment was conducted on the rice–wheat cropping system at four locations in India. Trends in partial factor productivity of applied nitrogen, benefit : cost ratio of fertilizer application, grain yield, changes in soil organic carbon, and available nitrogen (N), phosphorus (P) and potassium (K) were studied in control (N0P0K0), N (N120P0K0), NP (N120P80K0), NK (N120P0K40) and NPK (N120P80K40) fertilizer treatments. On average at all locations, continuous rice–wheat cropping for 16 years decreased the yield of rice by 57% in unfertilized plots and by 32% in plots receiving nitrogen and phosphorus fertilizers. Over the same period wheat yields only declined in unfertilized plots by 18%; in plots receiving nitrogen, phosphorus and potassium yields increased by 18% and they increased by 33.6% in plots receiving nitrogen and phosphorus fertilizer. Partial factor productivity of applied nitrogen (the ratio of output value to the cost of a specific input) exhibited similar trends. Profit from fertilizer application, however, increased over the 16-year cycle by 130% in rice and by 262% in wheat in the treatment given nitrogen and phosphorus fertilizers. The long-term rice–wheat cropping system became depleted in soil organic carbon and available nitrogen and phosphorus at two locations but increased in organic carbon, available nitrogen and potassium at the third location. The available phosphorus and potassium content of the soil also increased at the fourth location.