Although tropical peatlands are huge carbon reservoirs, they are threatened by climate change and anthropogenic disturbances. Here, we assessed two contrasting peatland sites in the Philippines in terms of aboveground biomass and carbon content, soil carbon stock, and CO2 fluxes in the soils. The Caimpugan peatland in Agusan del Sur was considered the ‘undisturbed’ site, while the Bambanin peatland in Mindoro Oriental was the ‘disturbed’ site. The aboveground biomass at the undisturbed site was 35.8 ± 30.0 Mg ha−1) while at the disturbed site, it was 2.0 Mg ha−1 ± 1.9 Mg ha−1. The aboveground C content at the undisturbed site varied from 1.29 Mg C ha−1 to 37.2 C Mg ha−1, while the disturbed site only ranged from 0.1 Mg C ha−1 to 2.1 Mg C ha−1. A trend of increasing soil carbon content as the soil gets deeper was observed in both sites. At the undisturbed site, the average soil carbon content was 750 ± 710 Mg ha−1 and 595 ± 406 Mg ha−1 at the disturbed site. In terms of soil carbon emission, the undisturbed site had 3.6 ± 3.0 g C m−2d−1 and was only one-third the emission rate at the disturbed site (11.2 ± 6.4 g C m−2d−1). Our study highlights the dire condition of a disturbed peatland in terms of vegetation/soil carbon dynamics. We underscored the need to address the pressing issues on peatland drainage, agricultural activities, and human settlement within the peatland sites geared towards effectively managing this important carbon reservoir in the Philippines.