Abstract: Traditional irrigated double-rice cropping systems have to cope with reduced water availability due to changes of climate and economic conditions. To quantify the shift in CH4 and N2O emissions when changing from traditional to diversified double cropping-systems, an experiment including flooded rice, non-flooded “aerobic” rice and maize was conducted during the dry season (February–June 2012) in the Philippines. Two automated static chamber–GC systems were used to continuously measure CH4 and N2O emissions in the three cropping systems of which each included three different nitrogen fertilization regimes. Turning away from flooded cropping systems leads to shifts in greenhouse gas emissions from CH4 under wet soil to N2O emissions under drier soil conditions. The global warming potential (GWP) of the non-flooded crops was lower compared to flooded rice, whereas high CH4 emissions under flooded conditions still override enhanced N2O emissions in the upland systems. The yield-scaled GWP favored maize over aerobic rice, due to lower yields of aerobic rice. However, the lower GHG emissions of upland systems are only beneficial if they are not overwhelmed by enhanced losses of soil organic carbon.