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This paper evaluates the potential effects of farmers' species preferences on carbon stock in cocoa-based agroforestry systems (CAFS) in the Central Region of Cameroon. To achieve this goal, the species composition and structural variables of two land-use systems were investigated using 26 plots of 30 m × 30 m each, of which 20 were distributed in CAFS and 6 in adjacent secondary forests. Allometric models were used to estimate the species aboveground and root carbon stock. Ordination analysis indicated three types of species management systems: high-density timber and fruit trees; high-density Musaceae, palms and other shading trees; and low-density timber and fruit trees. The average densities of cocoa shading trees and shrubs were 234 ± 136 and 843 ± 360 individuals' ha−1, respectively. Thus, the average potential carbon stock of the sampled CAFS was estimated at 186.97 ± 86.06 Mg C ha−1, 22% representing the root carbon stock. The transformation of secondary forest into various species management systems decreased the aboveground carbon by 18–34%. The annual rate of carbon accumulation estimated based on ring analyses was within the range 2.32–13.74 Mg C ha−1 year−1. The monetary value of the total carbon stored and the carbon accumulation rate were US$4042 ha−1and US$159 ha−1year−1, respectively. [ABSTRACT FROM AUTHOR]