Tropical forests play a significant role in climate change by sequestrating atmospheric carbon dioxide. However, deforestation and forest degradation adversely affect these forests’ carbon stocks. Reports indicate that anthropogenic activities have led to forest degradation and deforestation in Boabeng Fiema Monkey Sanctuary (BFMS) and Kogyae Strict Nature Reserve (KSNR). This study assessed the effects of these activities on BFMS and KSNR carbon stocks. Using satellite imagery, field measurements and allometric models, carbon stocks of the study area were assessed from 1992 to 2023, revealing significant losses attributed to anthropogenic activities such as hunting, farming and charcoal burning. BFMS experienced a total loss of 40,236 Mg C, while KSNR lost 272,109 Mg C. The closed forests had the highest carbon stock amongst the different vegetation types, with soil representing the most significant carbon pool in the protected areas, revealing the influence of vegetation structure on carbon sequestration and the need for soil conservation. The substantial carbon sequestration potential observed in the different vegetation types of the study area indicates that the Forest-Savannah Transition Zone is a prospective area for climate change mitigation aligning with the Sustainable Development Goals (Goals 13 and 15) and the National Climate Change Policy of Ghana. These findings provide valuable insights for carbon trading and biodiversity conservation, emphasizing the potential of nature-based solutions in addressing global climate challenges.