Abstract. Peat surface CO2 emission, groundwater table depth and peat temperature were monitored for two years along transects in an Acacia plantation on thick tropical peat (>4 m) in Sumatra, Indonesia. A total of 2300 emission measurements were taken at 144 locations, over a 2 year period. The autotrophic root respiration component of CO2 emission was separated from heterotrophic emission caused by peat oxidation in three ways: (i) by comparing CO2 emissions within and beyond the tree rooting zone, (ii) by comparing CO2 emissions with and without peat trenching (i.e. cutting any roots remaining in the peat beyond the tree rooting zone), and (iii) by comparing CO2 emissions before and after Acacia tree harvesting. On average, the contribution of autotrophic respiration to daytime CO2 emission was 21% along transects in mature tree stands. At locations 0.5 m from trees this was up to 80% of the total emissions, but it was negligible at locations more than 1.3 m away. This means that CO2 emission measurements well away from trees were free of any autotrophic respiration contribution and thus represent only heterotrophic emissions. We found daytime mean annual CO2 emission from peat oxidation alone of 94 t ha−1 y−1 at a mean water table depth of 0.8 m, and a minimum emission value of 80 t ha−1 y−1 after correction for the effect of diurnal temperature fluctuations, which may result in a 14.5% reduction of the daytime emission. There is a positive correlation between mean long-term water table depth and peat oxidation CO2 emission. However, no such relation is found for instantaneous emission/water table depth within transects and it is clear that factors other than water table depth also affect peat oxidation and total CO2 emissions. The increase in the temperature of the surface peat due to plantation establishment may explain over 50% of peat oxidation emissions. Our study sets a standard for greenhouse gas flux studies from tropical peatlands under different forms of agricultural land management. It is the first to purposefully quantify heterotrophic CO2 emissions resulting from tropical peat decomposition by separating these from autotrophic emissions. It also provides the most scientifically- and statistically-rigorous study to date of CO2 emissions resulting from anthropogenic modification of this globally significant carbon rich ecosystem. Our findings indicate that past studies have underestimated emissions from peatland plantations, with important implications for the scale of greenhouse gas emissions arising from land use change, particularly in the light of current, rapid agricultural conversion of peatlands in the Southeast Asian region.