Despite evidence that cocoa agroforests are composed of different types of associated plants leading to varieties of structures, few studies have been done to assess the implications of these variations on carbon stocks. The current studies profile the carbon storage of cocoa agroforests in Southern Cameroon by: (1) evaluating the carbon stocks of cocoa agroforests in different ecological zones (Yaoundé, Mbalmayo, and Ebolowa), (2) evaluating the carbon stocks of cocoa agroforests under different management methods, (3) evaluating the contribution of some plant species to carbon sequestration inside cocoa agroforests, and (4) identifying the carbon stocks of some important species. Inside the cocoa agroforests of Southern Cameroon, associated plants store around 70% of the carbon. Cocoa agroforests with timber and NWFP (Non-Wood Forest Products) store more than twice what is found in systems rich with Musa and oil palm. In these systems, timber and NWFP store more than 2.5 times what is found in cocoa systems with high densities of cocoa, and such systems with timber and NWFP store more than 3.3 times the carbon of unshaded cocoa orchards.