The increase in global climate variability due to greenhouse gas (GHG) emissions, especially CO2, has endangered both the environment and human health. In this context, it is important to quantify the carbon balance of anthropogenic activities, in terms of both carbon emission and carbon fixation. The aim of this study was to estimate the anthropogenic CO2 emissions and aboveground carbon stocks in agroforestry systems of cocoa (Theobroma cacao L.) in the southern Peruvian Amazon, specifically in Madre de Dios. Nine agroforestry systems (AFS) of 4-7 years of age were selected, composed of T. cacao in association with timber, non-timber and fruit tree species. CO2 emissions were estimates based on interviews with landowners, considering fuels, fertilizers, herbicides, and domestic use of firewood, charcoal, gas and electricity. To estimate carbon stocks, we calculate aboveground biomass, litter biomass and biomass of annual cocoa bean production. The density of T. cacao varied between 530-1160 individuals/ha with ten other associated species at lower densities. The aboveground carbon stock in AFS ranged from 7.7 to 13.7 Mg/ha and the carbon fixation rate ranged from 1.5 to 3 Mg/ha/year. Total emissions ranged from 0.12-2.15 Mg CO2e/ha/yr, with fuel use being the main source of emissions (up to 98%). Fixation rates ranged from 12.8-23.8 Mg CO2e/ha/year. CO2e fixation rates were significantly higher than emissions in every AFS. The results suggest that AFS did not have a negative impact on the environment. The study highlights the importance of AFS within the context of climate change and the increasing environmental impact of conventional agricultural systems. Therefore, our results will be useful in making sustainable public policy decisions and aligning them with low-carbon objectives, thereby increasing the economic and ecological resilience of agricultural areas in the Peruvian Amazon. The study shows that the assessed AFSs had a positive overall aboveground carbon balance. Emission rates were low, and fuel use was present in all the AFS and represented the largest source of CO2 emissions. Therefore, by harboring tree species, the AFS would allow for climate change adaptation and mitigation strategies.