In the climate change context, the reduction of forest area under the influence of cacaoculture is a growing problem. In Côte d’Ivoire, mitigating the effects of climate change in cacaoculture requires the introduction and preservation of woody species in plantations, in association to cocoa trees. However, the current intensification of land use is leading to a reduction of the number of trees associated to cocoa trees and the contribution of this woody flora to the mitigation of the effects of climate change is unclear. Our study aimed to assess the carbon storage of the associated woody species and to characterize the determinants of carbon storage. The circumference at 1.30 m above soil and total height of all individuals taller than 2 m in height were measured in 15 squares of 2 400 m2 for the associated woody stand and in 15 sub-squares of 800 m2 for the cocoa stand. The results showed that the carbon storage of the associated woody stand is 5 times higher than that the cocoa stand and recorded for large trees (diameter > 20 cm; height >8 m) such as Antiaris toxicaria, Ricinodendron heudelotii and Persea americana. Also, this high carbon storage is mainly due to the diameter and total height of the tree and not to the number of individuals. The association of large-scale species with cocoa trees could guarantee the resilience of cocoa agroforestry systems with trees.