Abstract Effects of four years of inorganic and organic nitrogen (N) management on the emission of three major greenhouse gases (GHGs): methane (CH 4 ), carbon dioxide (CO 2 ) and nitrous oxide (N 2 O), and on soil labile carbon fractions such as water-soluble carbon (C, WSC), microbial biomass carbon (MBC), KMnO 4 oxidizable organic carbon (KMnO 4 -C), carbon management index (CMI) and soil carbon storage were investigated in a flooded rice ( Oryza sativa L.) field in India. The treatments included an unfertilized control, inorganic nitrogen fertilizer, rice straw + inorganic nitrogen fertilizer and rice straw + green manure. Maximum global warming potential (GWP) (10,188 kg CO 2  equivalent ha −1 ) was determined for the combined application of rice straw and green manure. Total carbon content and carbon storage in the topsoil were significantly increased for the rice straw + inorganic nitrogen fertilizer treatment. The combined application of rice straw and green manure was more effective in increasing WSC, MBC, KMnO 4 -C concentrations and CMI than the inorganic fertilizer treatments, although it increased gaseous carbon emission. The combined application of rice straw and an inorganic fertilizer was most effective in sequestrating soil organic carbon (1.39 Mg ha −1 ), resulting in a higher grain yield. Therefore, it could be the best option for improving productivity and carbon storage in the rice–rice cropping system.

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