Deforested and converted tropical peat swamp forests are susceptible to fires and are a major source of greenhouse gas (GHG) emissions. However, information on the influence of land-use change (LUC) on the carbon dynamics in these disturbed peat forests is limited. This study aimed to quantify soil respiration (heterotrophic and autotrophic), net primary production (NPP), and net ecosystem production (NEP) in peat swamp forests, partially logged forests, early seral grasslands (deforested peat), and smallholder-oil palm estates (converted peat). Peat swamp forests (PSF) showed similar soil respiration with logged forests (LPSF) and oil palm (OP) estates (37.7 Mg CO2 ha−1 yr−1, 40.7 Mg CO2 ha−1 yr−1, and 38.7 Mg CO2 ha−1 yr−1, respectively), but higher than early seral (ES) grassland sites (30.7 Mg CO2 ha−1 yr−1). NPP of intact peat forests (13.2 Mg C ha−1 yr−1) was significantly greater than LPSF (11.1 Mg C ha−1 yr−1), ES (10.8 Mg C ha−1 yr−1), and OP (3.7 Mg C ha−1 yr−1). Peat swamp forests and seral grasslands were net carbon sinks (10.8 Mg CO2 ha−1 yr−1 and 9.1 CO2 ha−1 yr−1, respectively). In contrast, logged forests and oil palm estates were net carbon sources; they had negative mean Net Ecosystem Production (NEP) values (−0.1 Mg CO2 ha−1 yr−1 and −25.1 Mg CO2 ha−1 yr−1, respectively). The shift from carbon sinks to sources associated with land-use change was principally due to a decreased Net Primary Production (NPP) rather than increased soil respiration. Conservation of the remaining peat swamp forests and rehabilitation of deforested peatlands are crucial in GHG emission reduction programs.