Reducing methane (CH4) emission from paddy rice production is an important target for many Asian countries in order to comply with their climate policy commitments. National greenhouse gas (GHG) inventory approaches like the Tier-2 approach of the Intergovernmental Panel on Climate Change (IPCC) are useful to assess country-scale emissions from the agricultural sector. In paddy rice, alternate wetting and drying (AWD) is a promising and well-studied water management technique which, as shown in experimental studies, can effectively reduce CH4 emissions. However, so far little is known about GHG emission rates under AWD when the technique is fully controlled by farmers. This study assesses CH4 and nitrous oxide (N2O) fluxes under continuous flooded (CF) and AWD treatments for seven subsequent seasons on farmers’ fields in a pumped irrigation system in Central Luzon, Philippines. Under AWD management, CH4 emissions were substantially reduced (73% in dry season (DS), 21% in wet season (WS)). In all treatments, CH4 is the major contributor to the total GHG emission and is, thus, identified as the driving force to the global warming potential (GWP). The contribution of N2O emissions to the GWP was higher in CF than in AWD, however, these only offset 15% of the decrease in CH4 emission and, therefore, did not jeopardize the strong reduction in the GWP. The study proves the feasibility of AWD under farmers’ management as well as the intended mitigation effect. Resulting from this study, it is recommended to incentivize dissemination strategies in order to improve the effectiveness of mitigation initiatives. A comparison of single CH4 emissions to calculated emissions with the IPCC Tier-2 inventory approach identified that, although averaged values showed a sufficient degree of accuracy, fluctuations for single measurement points have high variation which limit the use of the method for field-level assessments.