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Rice (Oryza sativa L.) is cultivated as a major crop in most Asian countries and its production is expected to increase to meet the demands of a growing population. This is expected to increase greenhouse gas (GHG) emissions from paddy rice ecosystems, unless mitigation measures are in place. It is therefore important to assess GHG mitigation potential whilst maintaining yield. Using the process-based ecosystem model DayCent, a spatial analysis was carried out in a rice harvested area in Bangladesh for the period 1996 to 2015, considering the impacts on soil organic carbon (SOC) sequestration, GHG emissions and yield under various mitigation options. An integrated management (IM, a best management practice) considering reduced water, tillage with residue management, reduced mineral nitrogen fertilizer and manure, led to a net offset by, on average, −2.43 t carbon dioxide equivalent (CO2-eq.) ha−1 year−1 (GHG removal) and a reduction in yield-scaled emissions intensity by −0.55 to −0.65 t CO2-eq. t−1 yield. Under integrated management, it is possible to increase SOC stocks on average by 1.7% per year in rice paddies in Bangladesh, which is nearly 4 times the rate of change targeted by the “4 per mille” initiative arising from the Paris Climate Agreement.