Use of organic amendments such as farmyard manure (FYM), green manure (GM) and crop residues is important to improve soil health and reduce the dependence on synthetic chemical fertilizer. However, these organic amendments also effect the emissions of greenhouse gas (GHG) from soil. Influence of different organic amendments on emissions of GHG from soil and their global warming potential (GWP) was studied in a field experiment in rice–wheat cropping system of Indo-Gangetic plains (IGP). There was 28% increase in CH 4 emissions on addition of 25% N through Sesbania GM along with urea compared to urea alone. Substitution of 100% inorganic N by organic sources lead to a 60% increase in CH 4 emissions. The carbon equivalent emission from rice–wheat systems varied between 3816 and 4886kg C equivalentha −1 depending upon fertilizer and organic amendment. GWP of rice–wheat system increased by 28% on full substitution of organic N by chemical N. However, the C efficiency ratios of the GM and crop residue treatments were at par with the recommended inorganic fertilizer treatment. Thus use of organic amendments along with inorganic fertilizer increases the GWP of the rice–wheat system but may improve the soil fertility status without adversely affecting the C efficiency ratio. However, the trade-off between improved yield and soil health versus GHG emissions should be taken into account while promoting the practice of farming with organic residues substitution for mineral fertilizer.