Currently, the economic profitability of cocoa is being affected by the increasing incidence of pests, low selling prices, high production costs, and the presence of cadmium in cocoa farms, posing a potential risk of crop abandonment. Therefore, the objective of the present research was to evaluate the economic profitability of carbon sequestration of fine-aroma cacao agroforestry systems in Amazonas, Peru, using the economic indicators of NPV, EIRR, and the benefit–cost ratio. For this purpose, 53 small cocoa producers of the APROCAM cooperative were involved, from which data were obtained on the general characteristics of the production system, production and maintenance costs, indirect costs, and administrative costs; in addition, the costs of implementation and maintenance of an environmental services project were calculated to finally make a cash flow projected over 5 years. As part of the results, the economic analysis was carried out on 104.25 hectares of cocoa belonging to the total number of farmers evaluated, who reported an average yield of 957.32 kg of dry cocoa per he. In addition, it was found that the production cost is PEN 3.91/kg of dry cocoa, and the average selling price is PEN 7.38/kg of dry cocoa. After the economic analysis, it was found that the implementation of an environmental services project is profitable (NPV = PEN 1,454,547.8; EIRR = 44% and B/C = 1.86). These results open up an opportunity for cocoa farmers to diversify and increase their income by contributing to climate change mitigation.