The study aims to analyze the management, diversity and the uses of shade trees and then to evaluate the carbon stock in the woody biomass of cocoa and rubber farms. Density and diversity of shade trees were evaluated in 54 plots of 2500 m2 each, distributed in different cocoa and rubber farms which age varies from one year to more than 15 years. In addition, an investigation was carried out among the peasants to determine the uses of shade trees. The amount of carbon stored in woody biomass of these farms is calculated using allometric models of biomass. In total, 20 species of shade trees were inventoried in cocoa farms and 10 in rubber farms. Ceiba pentandra (L.) Gaertn. and Persea Americana Mill. are the most important species of these agrosystems. In general, the shade trees provide medical and food products, firewood and timber to farmers. These trees also prevent desiccation of young crop plants and provide nitrogen to soil. The average amount of carbon stored in woody biomass ranges from 50.85 to 145.14 tC/ha in cocoa farms and from 7.04 to 176.68 tC/ha in rubber farms. Shade trees contribute more than 87 % of this amount of carbon in cocoa farms, and only about 17 % in rubber farms. Agroforestry practice in perennial farms contributing to the conservation of multipurpose tree species and would boost the carbon stock in the agricultural sector.