Currently, extensive areas of tropical peatland in Southeast Asia are being developed for large-scale sago and oil palm plantation. However, their environmental impact is still uncertain. Thus, greenhouse gas (CO2, CH4, and N2O) fluxes from three ecosystems, namely mixed peat swamp forest, sago (Metroxylon sagu) and oil palm (Elaeis guineensis) plantation on tropical peatland of Sarawak, Malaysia were measured monthly over 12 months using a closed chamber technique. On an annual basis, the soil CO2 flux was highest in the forest ecosystem with an estimated production of 2.1 kg C m-2 yr-1 followed by oil palm at 1.5 kg C m-2 yr-1 and sago at 1.1 kg C m-2 yr-1. Both forest and sago were CH4 sources with an emission of 18.34 mg C m-2 y-1 and 180 mg C m-2 y-1, respectively. However, the oil palm ecosystem was a CH4 sink with an uptake rate of -15.14 mg C m-2 y-1. Highest annual N2O emissions were observed in the sago ecosystem with a production rate of 3.3 kg N ha-1 y-1, followed by oil palm ecosystem at 1.2 kg N ha-1 y-1 and forest ecosystem at 0.7 kg N ha-1 y-1. A regression tree approach showed that CO2 flux in each ecosystem were related to different underlying environmental factors. They were relative humidity for forest, soil temperature at 5 cm for sago and water-filled pore space for oil palm. For CH4, they were relative humidity for forest and water table for both sago and oil palm ecosystems. Multiple regression analysis showed that different variables regulated N2O production in each ecosystem. The key factors influencing N2O emissions in the forest ecosystem were water table and NH4+ concentration at 25-50 cm, soil temperature at 5 cm and nitrate concentration at 0-25 cm in the sago ecosystem, and water-filled pore space (WFPS), soil temperature at 5 cm and NH4+ concentrations at 0-25 cm in the oil palm ecosystem. The results showed that there were no dominant environmental controlling factors in each GHG flux across the three ecosystems. This implied that the soil GHG fluxes in tropical peatland were dependent on the environmental changes that were instituted to maximize crop production.