Purpose <p>Organic amendments for substituting chemical fertilizers (CF) have many environmental benefits; however, organic inputs increase methane (CH₄) emissions from rice (<i>Oryza sativa</i> L.) fields. To address this concern, this study aimed to suggest multiple measures to mitigate CH₄ for organic rice production by analyzing literature data on the effects of agricultural practices on the CH₄ emissions and rice yields of paddies amended with organic inputs.</p> Methods <p>We analyzed data on the changes in the rice yields and CH₄ emissions as affected by the types of organic inputs (rice straw, RS; green manure, GM; and livestock manure or compost, LMC) together with various agricultural practices, including the timing of organic input application (fallow vs. cropping seasons), soil drying, and the application of silicate fertilizer and biochar.</p> Results <p>Literature data showed that GM application produced rice yields comparable to those with CF while increasing CH₄ emissions compared to RS and LMC applications. Both soil drying and incorporating organic inputs in the fallow season effectively mitigated CH₄ emissions with marginal changes in the rice yield compared to CF. Although silicate fertilizer mitigated CH₄ emissions from CF-amended soils, it was indicated that CH₄ emissions may also increase by silicate fertilizer through the improved rice growth. It was also suggested that the application of biochar alone or combined with soil drying could further mitigate CH₄ emissions from organic-amended soils. These results suggested that soil drying and application of organic inputs in the fallow season are most feasible measures for sustainable rice production using organic inputs with CH₄ mitigation.</p> Conclusions <p>The combined implementation of multiple agricultural practices including extended soil drying, application of organic input in the fallow season, and application of biochar needs to be futher investigated to take full advantage of using organic inputs to substitute CF.</p>