Flooded rice production is crucial to global food security, but there are associated environmental concerns. In particular, it is a significant source of methane (CH4) and nitrous oxide (N2O) emissions and a large consumer of water resources, while arsenic levels in the grain are a serious health concern. There is also a tendency to use more organic fertilisers to close nutrient cycles, posing a threat of even higher GHG emissions and grain arsenic levels. It has been shown that alternate wetting and drying (AWD) water management reduces both water use and GHG emissions, but success at maintaining yields varies. This study tested the effect of early AWD (e-AWD) versus continuous flooding (CF) water management practices on grain yields, GHG emissions and grain arsenic levels in a split-plot field experiment with organic fertilisers under organic management. The treatments included: i) farmyard manure, ii) compost, and iii) biogas digestate, alone or in combination with mineral fertiliser. The e-AWD water regime showed no difference in yield for the organic treatments. Yields significantly increased by 5–16 % in the combination treatments. Root biomass and length increased in the e-AWD treatments up to 72 and 41 %, respectively. The e-AWD water regime reduced seasonal CH4 emissions by 71–85 % for organic treatments and by 51–76 % for combination treatments; this was linked to a 15–47 % reduction in dissolved organic carbon (DOC), thereby reducing methanogenesis. N2O emissions increased by 23–305 % but accounted for <20 % of global warming potential (GWP). Area and yield-scaled GWPs were reduced by 67–83 %. The e–AWD regime altered soil redox potentials, resulting in a reduction in grain arsenic and lead concentrations of up to 66 % and 73 % respectively. Grain cadmium levels were also reduced up to 33 % in organic treatments. Structural equation modelling showed that DOC, redox, ammonium and root biomass were the key traits that regulated emissions and maintained yield. Despite the fact that the experiment was conducted in the dry-season when soil moisture conditions can be relatively well-controlled, our findings should be confirmed in multi-year studies in farmers’ fields. These results suggest that in flooded rice systems receiving organic amendments or organic management, the e-AWD water regime can achieve multiple environmental and food safety objectives without compromising yield.