Increased use of irrigation and nitrogen (N) in rice and wheat would increase productivity. It would also enhance the emission of greenhouse gases from soil causing global warming and climate change. This study quantified the trade-offs between increased production with N fertilizer and irrigation application and the global warming potential (GWP) in the major rice and wheat growing regions of India. The InfoCrop model was used to simulate yield and GWP of rice and wheat for five regions in the country for two climatic scenarios i.e., current (1990–1999) and future (2050), two irrigation practices i.e., supply-driven irrigation (SDI) and demand-driven irrigation (DDI), and 10 levels of N and organic manure. Rice and wheat productivity of India can be increased from their current productivity of 3.26 and 2.73 Mg ha−1 to 5.66 and 6.15 Mg ha−1, respectively with increased irrigation and N use. But this would increase the GWP by 27 and 40%, respectively. In spite of the increased GWP the carbon efficiency ratio (CER) would increase from the current values of 0.67 and 0.85 to 1.06 and 1.75 in rice and wheat, respectively. Thus there is a ‘win-win’ situation in terms of increased CER for increasing productivity. These situations need to be identified to harness the benefit with more rational management practices including efficient use of irrigation and N, the major drivers for yield and GWP.