Peat C loss in Indonesia has never been estimated using the C stock change method in a synchronic experiment because of difficulty in Identifying an after-Land Use Change (LUC) location with an initial peat depth similar to that of the before-LUC location due to substantial spatial variability of peat depth, lack of maps locating the position of peat domes and sporadic presence of pristine peatlands at close distance to converted lands. Nevertheless, indirect methods so-called proxy variables or __ampersandsignldquo;proxies__ampersandsignrdquo; can be used for assessing the emission reduction and establishing carbon sequestration scenarios. The vegetation proxy approach provides the basis for peatland GHG accounting which covers all main factors that determines ecosystem level carbon dynamics. Therefore we recommend carbon stocks in soil and biomass as a proxy tool for developing carbon sequestration model which is a more conservative approach, easily adaptable and having other associated benefits like resource inventory and national level peat swamp forest (PSF) mapping. This can be done for both PSF already converted and also for developing carbon markets and climate change mitigation scenarios in future. This involves a synchronic experiment of carbon stock determination and comparison by taking PSF-vegetation and soil in intact-state versus any land uses in post-converted statuses. This methodology disregards the debate of separating heterotrophic and autotrophic respiration and instrumental shortcomings for flux measurement; instead the net CO2 emission overtime time can be estimated as the difference of carbon stocks in land units with similar permanent soil characteristics but different management interventions today.