Afforestation of savannah is suggested as an approach to help addressing climate change mitigation through increased carbon (C) storage. Previous studies in Central Cameroon evidenced farmers’ ability to realize afforestation by establishing cocoa-based agroforestry systems (cAFS) on humid savannah. In this forest-savannah transition zone, we studied an 80 years chronosequence of cAFS to assess C dynamics. We selected cAFS established after forest or savannah, and we used local forest and savannah patches as controls. Aboveground carbon (AGC) was highest in the forests (118 Mg C ha−1) and lowest in the savannahs (8 Mg C ha−1). Systems established after forest (F-cAFS) revealed a mean AGC 40% lower than that of forests and did not evolve with time. The AGC of cAFS established after savannah (S-cAFS) increased with time and reached the mean AGC of F-cAFS (72 Mg C ha−1) after ca. 75 years. Soil organic carbon (SOC) concentration depended on clay content (R2 = 0.55, P < 0.001). The SOC concentration of F-cAFS did not evolve with time and revealed no difference with forest. In S-cAFS, considering a time of about 80 years after afforestation, the average annual increase in SOC concentration in the 0–15 cm layer ranged from 7.3‰ in soils with low clay content (10–15%) (R2 = 0.60, P < 0.01) to 9.5‰ in soils with higher clay content (20–25%). No significant change in SOC concentration was found for the 15–30 cm layer. Overall, S-cAFS revealed to store and maintain significant levels of C both in the aboveground biomass and in the soil. Such an afforestation thus appeared as a valuable local strategy to combine cocoa and other perennial plant productions with C storage while avoiding deforestation.