Tropical wetlands such as peat swamp forests (PSFs) have been known globally as one of the carbon (C)-rich ecosystems. However, there is still a lack of understanding on the C cycle in PSFs, especially in association with land use and cover changes (e.g., ecosystem degradation and restoration). This study presents the C stocks, removals, and emissions dataset, as well as the determining factors from an early restoration stage of secondary tropical PSFs in Central Kalimantan. We assessed various biophysical parameters such as forest structure, above- and belowground C-stocks, aboveground primary productivity, total and heterotrophic soil respirations, and groundwater level (GWL). We found that tree density varied from 1200 to 1825 trees per hectare (ha) across the plots, whereas the mean of stand basal area was 32.86 ± 4.72 m2 ha-1. Mean ecosystem C stocks in the study site was 1752 ± 401 Mg-C ha-1, of which 93% was stored in belowground organic peat soils. A mean aboveground litterfall production of 4.6 ± 0.5 Mg-C ha-1 year-1 and biomass C sequestration through tree diameter increment with 2.7 ± 0.5 Mg-C ha-1 year-1 was obtained. We observed slightly larger portion of annual mean total soil respiration with 14.2 ± 1.1 Mg-C ha-1 year-1 than heterotrophic respiration 11.1 ± 0.9 Mg-C ha-1 year-1, emphasizing the lower contribution of autotrophic respiration from the belowground rooting system. Findings imply that further conservation management efforts through ecosystem restoration may preserve C stored and enhance C input in PSFs substantially, and could be potentially included in national climate change mitigation strategies.