Organic soils are important carbon stocks. The conventional (dry) cultivation of these soils turns them into strong sources of greenhouse gas (GHG) emissions. For situations where restoration of natural land cover is not possible, solutions to this problem include the wet cultivation of these soils, reducing CO2 and N2O emissions. One option, paddy rice cultivation, has begun in the Swiss Central Plateau, which hitherto did not provide a suitable climate for wet rice. Wet rice is however associated with high CH4 emissions. These need to be quantified for this region, as the increased CH4 fluxes might negate the expected reductions in CO2 and N2O. Here, we quantify CH4 and N2O emissions from wet rice on organic soil with chamber measurements, in an outdoor mesocosm experiment in the Swiss Central Plateau, located in the cool temperate moist zone. We apply two water treatments (a high water table (WT) treatment, − 6 cm with mid-season drainage, and two medium WT treatments, − 11 and − 17 cm without mid-season drainage) and additionally test the use of a mineral cover layer to reduce N2O emissions. Additionally, a deeply-drained grassland treatment is used as a reference treatment. Annual CH4 emissions from rice cultivation are 6.2 g CH4.m-2.a-1 for the higher WT treatment, 6.4 g CH4.m-2.a-1 for the medium WT treatment and 2.4 g CH4.m-2.a-1 for the medium WT treatment with mineral cover. The corresponding N2O emissions are 203, 190 and 56 mg N2O-N.m-2.a-1, respectively. These results show that adding a mineral cover layer reduces annual emissions from both GHGs substantially. In total, the maximum increase in CH4 and N2O emissions resulting from rice cultivation, compared to the drained grassland treatment, is 2.3 t CO2-eq.ha-1.a-1. Expected CO2 emissions savings (derived from a literature-based model) due to a higher WT are a factor of 5–9 greater than this. We thus conclude that the cultivation of these organic soils in this region with wet rice could reduce their induced warming compared to their cultivation with (deeply drained) grassland.