Intermittent flooding (IF) of rice has been encouraged as an approach to reduce water use and methane emissions compared with continuous flooding (CF), but may involve trade-offs. This study compared the contrasting effect of IF and CF flooding regimes on emissions of methane (CH4), nitrous oxide (N2O) and ammonia (NH3), nitrogen use efficiency (NUE) and yield. A split plot design was used which assessed the effects of four different fertiliser types. The results suggest that converting from CF to IF irrigation does lower CH4 emissions (by approximately 18%); however, this comes at a cost. IF irrigation resulted in a significant decrease in grain yield, regardless of fertiliser type (6.1% in this study) and also a significant decrease in NUE (a drop of 22.5% when compared to CF). IF irrigation also resulted in a small, but statistically significant (t-test p < 0.01) increase in N2O emissions. Difference in NH3 emission between the flooding regimes was not statistically significant. Our study concludes that conversion from CF to IF irrigation methods may well reduce overall global warming potential of greenhouse gas emissions from rice production; however, yield penalties and nitrogen pollution are likely to increase as a result. Leaf colour chart based application of Neem coated urea may lower the yield scaled GHG emissions under CF irrigation and NH3 loss in IF irrigation.