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The cocoa tree (Theobroma cacao L.) is cultivated typically in agroforestry systems in close association with a rich list of tree species and other useful plants on the same plot. Cocoa based agroforestry systems are credited for stocking significant amounts of carbon and hence have the potential to mitigate climate change. Since cocoa yields decrease non-linearly with increasing shade, a need is to design optimal cocoa agroforestry systems with high yields and high carbon stocks. We estimated the carbon stocked in a network of 229 permanent sample plots in cacao-based agroforestry systems and natural forests in five Central American countries. Carbon stocks were fractioned by both system compartments (aboveground, roots, soil, litter, dead wood – fine and coarse, and total) and tree use/form (cocoa, timber, fruit, bananas, shade and ornamentals, and palms). Cocoa plantations were assigned to a five-class typology and tested for independence with growing region using contingency analysis. Most Central American cocoa plantations had mixed or productive shade canopies. Only 4% of cocoa plantations were full sun or rustic (cocoa under thinned natural forest). Cocoa tree density was low (548 ± 192 trees ha−1). Total carbon (soil + biomass + dead biomass) was 117 ± 47 Mg ha−1, with 51 Mg ha−1 in the soil and 49 Mg ha−1 (42% of total carbon) in aboveground biomass (cocoa and canopy trees). Cocoa trees accumulated 9 Mg C ha−1 (18% of carbon in aboveground biomass). Timber and fruit trees stored 65% of aboveground carbon. The annual rate of accumulation of carbon in aboveground biomass ranged between 1.3 and 2.6 Mg C ha−1 y−1. Trade-offs between carbon levels and yields were explored qualitatively using functional relationships documented in the scientific and technical literature, and expert knowledge. We argue that it is possible to design cocoa-based AFS with good yields (cocoa and shade canopy) and high carbon stock levels. The botanical composition of the shade canopy provides a large set of morphological and functional traits that can be used to optimize shade canopy design. Our results offer Central American cocoa producers a rigorous estimate of carbon stocks in their cocoa plantations. This knowledge may help them to certify and sell their cocoa, timber, fruits and other goods to niche markets with good prices. Our results will also assist governments and the private sector in (i) designing better legal, institutional and policy frameworks, local and national, promoting an agriculture with trees and (ii) contributing to the development of the national monitoring, reporting and verification systems required by the international community to access funding and payment for ecosystem services.