For agricultural purposes, the drainage and deforestation of Southeast Asian peatland resulted in high greenhouse gases’ (GHGs, e.g., CO2, N2O and CH4) emission. A peatland regenerating initiative, by rewetting and vegetation restoration, reflects evidence of subsequent forest recovery. In this study, we compared GHG emissions from three Malaysian tropical peatland systems under the following different land-use conditions: (i) drained oil palm plantation (OP), (ii) rewetting-restored forest (RF) and (iii) undrained natural forest (NF). Biweekly temporal measurements of CO2, CH4 and N2O fluxes were conducted using a closed-chamber method from July 2017 to December 2018, along with the continuous measurement of environmental variables and a one-time measurement of the soil physicochemical properties. The biweekly emission data were integrated to provide cumulative fluxes using the trapezoidal rule. Our results indicated that the changes in environmental conditions resulting from draining (OP) or rewetting historically drained peatland (RF) affected CH4 and N2O emissions more than CO2 emissions. The cumulative CH4 emission was significantly higher in the forested sites (RF and NF), which was linked to their significantly higher water table (WT) level (p < 0.05). Similarly, the high cumulative CO2 emission trends at the RF and OP sites indicated that the RF rewetting-restored peatland system continued to have high decomposition rates despite having a significantly higher WT than the OP (p < 0.05). The highest cumulative N2O emission at the drained-fertilized OP and rewetting-restored RF sites was linked to the available substrates for high decomposition (low C/N ratio) together with soil organic matter mineralization that provided inorganic nitrogen (N), enabling ideal conditions for microbial mediated N2O emissions. Overall, the measured peat properties did not vary significantly among the different land uses. However, the lower C/N ratio at the OP and the RF sites indicated higher decomposition rates in the drained and historically drained peat than the undrained natural peat (NF), which was associated with high cumulative CO2 and N2O emissions in our study.