Large areas of temperate peatlands are drained for agriculture and are strong sources of greenhouse gases (GHG). Paddy rice cultivation as a new cropping system in the cool temperate climate could offer an opportunity for continuing food production on these organic soils, possibly reducing carbon dioxide (CO2) and nitrous oxide (N2O) emissions by rewetting. However, methane (CH4) from paddy rice cultivation might impair the potential climate benefits. Here, the GHG fluxes of CO2, CH4, and N2O of paddy rice grown on organic soil with and without amended mineral cover, as well as in ley cultivated on drained organic soil as a reference, were quantified in an outdoor mesocosm experiment in Switzerland (cool temperate climate). Measurements were conducted with manual chambers for one year. Compared to ley under drained management, paddy rice cultivation reduced the net GHG balance by 36.1 %, from 32.7 (7.0) to 20.9 (2.7) t CO2 eq ha−1 yr−1. The GHG balance was dominated by CO2 whereas CH4 accounted for 8 % (54.3 (26.2) kg CH4 ha−1 yr−1). Most CO2 emissions occurred during the drained fallow period (mid-September–April). N2O emissions (0.9 (0.4) kg N2O-N ha−1 yr−1) were reduced by 83.9 % with paddy rice. Adding an amended mineral cover to organic soil slightly reduced the net GHG balance further, but not significantly. Multi-year studies on field-scale are required to generalize this study’s findings derived from a one-year mesocosm experiment. The results point towards paddy rice cultivation being a promising alternative to drained agriculture on temperate organic soils while maintaining food production and mitigating GHG emissions.