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In order to develop economically and environmentally sustainable productive activities, the effect of three agroforestry systems (SAF) of the cocoa crop was evaluated. The variable responses were the capture and storage of carbon, in the shrub, tree and soil biomass. The SAF of cocoa were from different physiographic units with ages, under 8 years, between 8 to 16 years and over 16 years. The statistical design was used completely at random, the allometric method; the organic carbon estimate was determined by the Walkley and Black method. The highest total carbon storage was reached by the SAF over 16 years with 344.24 t C / ha, the SAF between 8 and 16 years with 178.61 t C / ha, and the SAF under 8 years with 154.91 t C / ha. higher organic carbon was found in the soil in the SAF with cacao less than 8 years old, with 66.16 t C / ha between the soil layer of 0 to 10 cm. The economic analysis VAN, TIR and RB / C indicated that the best result was the SAF under 8 years with S /. 2627.66; 23.85%; and 1.40 respectively. The SAF over 16 years, obtained the S/. 1331.38, 21.64%, 1.21%, providing more environmental services. [ABSTRACT FROM AUTHOR]