The rice-maize system is a dominant cropping system of south Asia and consumes a considerable amount of fertilizer. The indiscriminate use of fertilizer particularly nitrogen (N) is degrading the soil health and polluting the environment. Lower N-use efficiency is a major problem and needs to be improved for higher yield, lower cost of cultivation and better environment. The grain quality is also altered by the N-application as N is a major constituent of protein. Studies on the effect of N-application on grain N-content is still lacking. We hypothesised that optimization of N application would result in economising N dose, improving yield and NUE and improving grain quality. Under that context, a field experiment was conducted with different doses of fertilizer N for rice and maize. Fertilizer N was applied at the rate of 0, 40, 80, 120, 160, 200 and 240 kg ha−1(N0–N240). An increase in grain yield was observed up to 80 and 160 kg ha−1for rice and maize, respectively. The N content of grain increased with N rates and a significant increase was noted in N200 (1.42%) being at par with N240 (1.49%) but significantly higher than others by 13–32%. With an increase of each kilogram of N, the grain N content increased by 14 and 20 μg (microgram) for rice and maize, respectively. The leaf N content registered a decreasing trend with the progress of the crop growth for both rice and maize. The agronomic efficiency (AE) of N initially increased with an increase in the rate of fertilizer N followed by a decrease with higher doses of N. Unlike the AE, the partial factor productivity (PFP) of N decreased gradually with an increase in the rate of fertilizer N. The chlorophyll content of flag leaves also registered an increasing trend with an increasing rate of fertilizer N. On the surface soil (0–15 cm), the treatments which received lower (N0, N40) and higher (N240) fertilizer N recorded a comparatively higher total soil N than other treatments. The mean NUE was 0.42 and 0.75 for rice and maize, respectively. The study suggests an economic fertilizer N rate of 165 and 167 kg N ha−1, for rice and maize, respectively. It also concludes that the grain N content can be altered by N-application rates though more research is needed.