The upcoming global mechanism for reducing emissions from deforestation and forest degradation in developing countries should include and prioritize tropical peatlands. Forested tropical peatlands in Southeast Asia are rapidly being converted into production systems by introducing perennial crops for lucrative agribusiness, such as oil-palm and pulpwood plantations, causing large greenhouse gas (GHG) emissions. The Intergovernmental Panel on Climate Change Guidelines for GHG Inventory on Agriculture, Forestry, and Other Land Uses provide an adequate framework for emissions inventories in these ecosystems; however, specific emission factors are needed for more accurate and cost-effective monitoring. The emissions are governed by complex biophysical processes, such as peat decomposition and compaction, nutrient availability, soil water content, and water table level, all of which are affected by management practices.