Tropical peatland ecosystems are a significant component of the global carbon cycle and feature a range of distinct vegetation types, but the extent of links between contrasting plant species, peat biogeochemistry and greenhouse gas fluxes remains unclear. Here we assessed how vegetation affects small scale variation of tropical peatland carbon dynamics by quantifying in situ greenhouse gas emissions over 1 month using the closed chamber technique, and peat organic matter properties using Rock-Eval 6 pyrolysis within the rooting zones of canopy palms and broadleaved evergreen trees. Mean methane fluxes ranged from 0.56 to 1.2 mg m ⁻²  h ⁻¹ and were significantly greater closer to plant stems. In addition, pH, ranging from 3.95 to 4.16, was significantly greater closer to stems. A three pool model of organic matter thermal stability (labile, intermediate and passive pools) indicated a large labile pool in surface peat (35–42%), with equivalent carbon stocks of 2236–3065 g m ⁻² . Methane fluxes were driven by overall substrate availability rather than any specific carbon pool. No peat properties correlated with carbon dioxide fluxes, suggesting a significant role for root respiration, aerobic decomposition and/or methane oxidation. These results demonstrate how vegetation type and inputs, and peat organic matter properties are important determinants of small scale spatial variation of methane fluxes in tropical peatlands that are affected by climate and land use change.