Indonesia has globally significant amount of forest cover and is a biodiversity hotspot but it also has one of the highest deforestation rates. In tropical regions, forests are increasingly being cleared and converted to agricultural fields and plantations. Agriculture is a major occupation in many developing countries, including Indonesia and a large proportion of which a smallholder farmers who traditionally practice swidden cultivation. This loss of forest cover leads to the losses of multiple benefits from these forests to the local population. The forests provide regulating functions by way of carbon (C) sequestration and play an important role in the greenhouse gas emissions and fluxes at a global scale. Deforestation and land degradation are exacerbating the climate change problem by releasing significant amounts of carbon dioxide (CO2) into the atmosphere. Agroforestry presents a practicable solution to these challenging problems as it can reduce vulnerability of smallholder farmers to climate variability while sequestering significant amounts of C, which would otherwise be emitted as CO2 emissions into the atmosphere. This study was conducted to quantify C stocks of agroforestry system (1 – 2 years), jungle rubber (young jungle rubber < 10 years and old jungle rubber > 50 years) and secondary forests (also approximately > 50 years) in Kapuas Hulu regency (West Kalimantan province) of Indonesia. Previous scientific research in this field has focused mainly on the measurement of aboveground living biomass. The focus of the present study was to estimate the C stocks of these land-use systems for the C pools in accordance to the IPPC guidelines, which are above- and belowground C-pools, dead wood and litter C as well as soil organic C (SOC). The study found that in general, there was an increase in Total C content from more intensively used land-use (agroforestry systems) to less intensively used land-use (secondary forest) with the exception of old jungle rubber which stored the highest Total C. The Total C stored in these ecosystems ranged from 80.41 ± 2.56 to 289.99 ± 26.50 Mg C ha-1. The most important carbon pool for the agroforestry systems and young jungle rubber was soil organic carbon, storing between 54.94 to 82.66% of Total C whereas, the overstorey pool stored the largest amount of carbon for the old jungle rubber and secondary forests (between 49.64 to 54.71%). ANOVA and multiple comparison test revealed that C stored in soil, overstorey, root and litter were significantly affected by land-use change. Deadwood and understorey carbon were unaffected by land-use conversion.