One way to mitigate climate change is by reducing atmospheric CO2 levels with the establishment of agroforestry systems (AFSs) that can capture and store atmospheric CO2. This study therefore estimated the carbon sequestration in two components, aboveground (cocoa trees, other tree species, and leaf litter) and soil, in 15 fine aroma cocoa AFSs in Amazonas, Peru. These cocoa AFSs had a minimum area of 1.5 ha and were distributed into three age groups (each group consisted of five systems or farms): young cocoa trees between 8 and 15 years old, middle-aged cocoa trees between 16 and 29 years old, and adult cocoa trees between 30 and more than 40 years old. Generalized linear mixed model (GLMM) analysis followed by Fisher’s LSD mean comparison test (p > 0.05) determined the significant level of total aboveground biomass and total carbon content in the AFSs’ components. The present findings confirm that Theobroma cacao, Mussa sp., Cordia sp., and Persea sp. were the most common species in all AFSs. Clearly, biomass and carbon content in Theobroma cacao and Cordia sp. increased slightly with age, while fruit species Mussa sp. and Persea sp. decreased with age. The total aboveground carbon stock in young cocoa tree systems (13.64 Mg ha−1) was lower than in middle-aged cocoa systems (20.50 Mg ha−1) and adult cocoa systems (24.86 Mg ha−1); nevertheless, no significant differences were found for any of the age ranges. On the other hand, carbon stocks in soil (up to 30 cm depth) in the AFSs ranged from 119.96 Mg ha−1 to 131.96 Mg ha−1. Meanwhile, the total carbon stored by aboveground and soil components in adults cocoa systems (156.81 Mg ha−1) was higher compared to middle-aged cocoa systems (140.60 Mg ha−1) and young cocoa systems (133.59 Mg ha−1), although no statistically significant differences were found. Eventually, the CO2 sequestration for young cocoa systems was 490.28 Mg ha−1, and middle-aged and adult cocoa system recorded more than 500 Mg ha−1 of CO2. Furthermore, these data can further be used by national governments, local governments, and organisations of producers, particularly in accessing payments for environmental services, which may improve economic incomes and contribute to climate change mitigation by reserving biomass and sequestering C from these agroforestry cocoa systems.