Oil palm plantations on peat and associated drainage generate sizeable GHG emissions. Current IPCC default emission factors (EF) for oil palm on organic soil are based on a very limited number of observations from young plantations, thereby resulting in large uncertainties in emissions estimates. To explore the potential of process-based modeling to refine oil palm peat CO₂ and N₂O EFs, we simulated peat GHG emissions and biogeophysical variables over 30 years in plantations of Central Kalimantan, Indonesia. The DNDC model simulated well the magnitude of C inputs (litterfall and root mortality) and dynamics of annual heterotrophic respiration and peat decomposition N₂O fluxes. The modeled peat onsite CO₂-C EF was lower than the IPCC default (11 Mg C ha^-1 yr^-1) and decreased from 7.7 ± 0.4 Mg C ha^-1 yr^-1 in the first decade to 3.0 ± 0.2 and 1.8 ± 0.3 Mg C ha^-1 yr^-1 in the second and third decades of the rotation. The modeled N₂O-N EF from peat decomposition was higher than the IPCC default (1.2 kg N ha^-1 yr^-1) and increased from 3.5 ± 0.3 kg N ha^-1 yr^-1 in the first decade to 4.7- 4.6 ± 0.5 kg N ha^-1 yr^-1 in the following ones. Modeled fertilizer-induced N₂O emissions were minimal and much less than 1.6% of N inputs recommended by the IPCC in wet climates regardless of soil type. Temporal variations in EFs were strongly linked to soil C:N ratio and soil mineral N content for CO₂ and fertilizer-induced N₂O emissions, and to precipitation, water table level and soil NH₄⁺ content for peat decomposition N₂O emissions. These results suggest that current IPCC EFs for oil palm on organic soil could over-estimate peat onsite CO₂ emissions and underestimate peat decomposition N₂O emissions and that temporal variation in emissions should be considered for further improvement of EFs.