The present field study investigated the effects of the system of rice intensification (SRI) on greenhouse gas emissions and rice yield, in the first field trial of its kind in Cambodia. The study was a 2 × 4 factorial design, including SRI and conventional management practices (CMP) with the following treatments: control, composted farmyard manure (FYM), mineral fertiliser (MF) and FYM + MF. The results indicated large seasonal variations of CH patterns during the growing season with a peak emission of about 1,300 mg CH m day under both production systems 2 weeks after rice transplanting. There was large temporal variability of CH fluxes from morning to midday. Emission of NO was below the detection limit in both systems. Under each production system, the highest seasonal emission of CH was under the FYM + MF treatment, namely 282 kg ha under CMP and 213 kg ha under SRI. Total CH emission under SRI practices was reduced by 22 % in the FYM treatment, 17 % in the MF treatment and 24 % in the FYM + MF treatment compared to CMP. There was no effect of water management on CH emission in the non-fertilized treatment. Grain yields were not significantly affected by the production system. Thus the yield-scaled global warming potential (GWP) was lower under SRI than CMP, namely 21 % in FYM and FYM + MF treatments, and 8 % in MF treatment. The application of mineral fertilisers moderately increased CH emission but significantly increased rice yields, resulting in a significantly lower yield-scaled-GWP compared to farmyard manure.