For countries' emission-reduction efforts under the Paris Agreement to be effective, baseline emission/removals levels and reporting must be as transparent and accurate as possible. For Indonesia, which holds among the largest area of tropical peatlands and mangrove forest in the world, it is particularly important for these high-carbon ecosystems to produce high-accuracy greenhouse gas inventory and to improve national forest reference emissions level/forest reference level. Here, we highlight the opportunity for refining greenhouse gas emission factors (EF) of peatlands and mangroves and describe scientific challenges to support climate policy processes in Indonesia, where 55 to 59% of national emission reduction targets by 2030 depend on mitigation in Forestry and Other Land Use. Based on the stock-difference and flux change approaches, we examine higher-tier EF for drained and rewetted peatland, peatland fires, mangrove conversions, and mangrove on peatland to improve future greenhouse gas flux reporting in Indonesia. We suggest that these refinements will be essential to support Indonesia in achieving Forest and Other Land Use net sink by 2030 and net zero emissions targets by 2060 or earlier.