Climate and land-use change alters greenhouse gas (GHG) fluxes of tropical peatlands, but the magnitude of these changes remains highly uncertain owing to limited measurements. We measured net ecosystem exchanges of carbon dioxide (CO2) and methane (CH4) as well as soil nitrous oxide (N2O) fluxes between mid-2016 to mid-2022 from Acacia crassicarpa plantation, degraded forest and intact forest within the same peat landscape to represent land-cover change trajectories in Sumatra, Indonesia. Here we report the first full plantation cycle GHG balance investigation undertaken in any fiber wood plantation on peatland globally. The Acacia plantation was found to have lower GHG emissions than the degraded peatland, which had a similar mean groundwater level, despite more intensive land-use. The GHG emissions from the Acacia plantation over a full plantation cycle (38.4 ± 2.3 tCO2eq ha−1 yr−1, average ± standard deviation) were two times higher than those from the intact forest (19.9 ± 1.9 tCO2eq ha−1 yr−1), but only around half of the current IPCC Tier 1 emission factor for this land-use. Observed emissions from intact forest imply that conversion of intact peatland to Acacia plantation has led to a net increase in GHG emissions of 18.5 ± 2.1 tCO2eq ha−1 yr−1 at our site. A relationship between CO2 fluxes and groundwater levels based on the eddy covariance measurements in tropical peatlands suggests that the existing relationships based on subsidence and soil chamber measurements may over-estimate both CO2 emissions and associated mitigation potentials.