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Tropical montane forests played an important role in the provision of ecosystem services. The intense degradation and deforestation for the need of agricultural land expansion result in a significant decline of forest cover. However, the expansion of agricultural land did not completely destruct natural forests. There remain forests inaccessible for agricultural and grazing purpose. Studies on these forests remained scant, motivating to investigate biomass and soil carbon stocks. Data of biomass and soils were collected in 80 quadrats (400 m2) systematically in 5 forests. Biomass and disturbance gradients were determined using allometric equation and disturbance index, respectively. The regression modeling is employed to explore the spatial distribution of carbon stock along disturbance and environmental gradients. Correlation analysis is also employed to identify the relation between site factors and carbon stocks. The result revealed that a total of 1655 individuals with a diameter of ≥ 5 cm, representing 38 species, were measured in 5 forests. The mean aboveground biomass carbon stocks (AGB CS) and soil organic carbon (SOC) stocks at 5 forests were 191.6 ± 19.7 and 149.32 ± 6.8 Mg C ha−1, respectively. The AGB CS exhibited significant (P < 0.05) positive correlation with SOC and total nitrogen (TN) stocks, reflecting that biomass seems to be a general predictor of SOCs. AGB CS between highly and least-disturbed forests was significantly different (P < 0.05). This disturbance level equates to a decrease in AGB CS of 36.8% in the highly disturbed compared with the least-disturbed forest. In all forests, dominant species sequestrated more than 58% of carbon. The AGB CS in response to elevation and disturbance index and SOC stocks in response to soil pH attained unimodal pattern. The stand structures, such as canopy cover and basal area, had significant positive relation with AGB CS. Study results confirmed that carbon stocks of studied forests were comparable to carbon stocks of protected forests. The biotic, edaphic, topographic, and disturbance factors played a significant variation in carbon stocks of forests. Further study should be conducted to quantify carbon stocks of herbaceous, litter, and soil microbes to account the role of the whole forest ecosystem.