Peatlands of Southeast Asia store large pools of carbon but the mechanisms of peat accumulation in tropical forests remain to be resolved. Patch dynamics and forest disturbance have seldom been considered as drivers that can amplify and dampen rates of peat accumulation. Here we used a modified piston corer, non-invasive geophysical measurements, and geochemical and paleobotanical techniques to establish the effect of tree fall on carbon accumulation rates in a peat swamp forest dominated by Shorea albida in Brunei (Borneo). Carbon initially accumulated in a mangrove forest at over 300 g C m−2 yr−1 but declined to less than 50 g C m−2 yr−1 with the establishment of a peat swamp forest. A rapid accumulation pulse of 720–960 g C m−2 yr−1 occurred around 1080 years ago as a tip-up pool infilled. Tip-up pools are common in the peatlands of northwest Borneo where windthrow and lightning strikes produce tree falls at a rate of 4 trees ha−1 every decade. A simulation model indicates that tip-up pools, which are formed across the entire forested peat dome, produce local discontinuities in the peat deposit, when peat is removed to create a pool and then rapidly filled with younger material. The resulting discontinuities in peat age at the base and sides of pool deposits obscure linkages between carbon accumulation rates and climate and require new approaches for paleo-environmental reconstructions. Our results suggest that carbon accumulation in tropical peat swamps may be based on fundamentally different peat forming processes than those of northern peatlands.