Mangrove forests are extremely productive, with rates of growth rivaling some terrestrial tropical rainforests. However, our understanding of the full suite of processes underpinning carbon exchange with the atmosphere and near shore-waters, the allocation of carbon in mangroves, and fluxes of non-CO2 greenhouse gases (GHGs) are limited to a handful of studies. This constrains the scientific basis from which to advocate for greater support for and investment in mangrove restoration and conservation. Improving understanding is urgently needed given the on-going landuse pressures mangrove forests face, particularly throughout much of Southeast Asia. The current study reduces uncertainties by providing a holistic synthesis of the net potential GHG mitigation benefits resulting from rehabilitating mangroves and established forests. Rehabilitating sites from two contrasting locations representative of high (Tiwoho) and low (Tanakeke) productivity systems on the island of Sulawesi (Indonesia) were used as case studies to compare against established mangroves. A carbon budget, allocation and pathways model was developed to account for inputs (carbon sequestration) and outputs (GHG emissions of CO2, N2O and CH4) to estimate Net Ecosystem Production (NEP) and Net Ecosystem Carbon Balance (NECB). Our results indicate that while Tiwoho's rehabilitating sites and established mangroves represent a significant carbon sink (−10.6 ± 0.9 Mg CO2e ha−1 y−1 and 16.1 Mg CO2e ha−1 y−1 respectively), the low productivity of Tanakeke has resulted in minimal reductions to date (0.7 ± 0.3 Mg CO2e ha−1 y−1). Including NEP from mangrove-allied primary producer communities (e.g. benthic algae) and the portion of dissolved inorganic carbon exported from mangroves (EXDIC) that remains within the water column may drive overall removals considerably upwards in established forests to −37.2 Mg CO2e ha−1 y−1. These values are higher than terrestrial forests and strengthen the evidence base needed to underpin the use of forest carbon financing mechanisms for mangrove restoration.