The function of tropical peatland as a carbon sink is a balance between peat accumulation and peat loss; however, various interacting factors are involved affecting this process. In this study, we collected and intensively radiocarbon dated peat cores from two peat domes, visualized their cross-sectional profiles of geochemical properties, and developed three macrocharcoal records from each peat dome. We find that the young (4500 y calBP) and shallow (6 m) coastal peat has a simple and linear age–depth relationship, showing stable accumulation of carbon during the late Holocene. In contrast, the older (ca. 40,000 y cal BP) and deeper (15 m) inland peat shows a more complex history, where we observed age reversals and hiatuses, likely caused by climate variability from the Last Glacial Maximum (LGM) to the Holocene. The charcoal record reveals a continuous presence of low-severity fire as indicated by charcoal morphotypes, though fire frequency increased after agriculture was established. An age reversal during the LGM was likely caused by a flood. Two periods of hiatuses occurred, each several millennia in length, at the end of the LGM and during the early Holocene. One cause of the hiatuses may have been a climatically halted peat formation from low precipitation and cooler climate during the LGM. Another cause may have been that severe fires consumed thousands of years of accumulated peat. If the hiatuses were entirely due to fire, the carbon released from these paleo-fire events (600 t C ha −1 ) suggests several times the impact of the most intense modern peat fires.