AbstractThe fine flavor cocoa (FFC) market offers additional income for small farmers. Despite the potential of several Latin American countries to produce FFC, their lack of standardized postharvest processes hinders compliance with high‐quality standards demanded by the FFC market, as these processes have a direct impact on cocoa's organoleptic characteristics. This work supports the design of a collective postharvest transformation model that coordinates the main steps in the cocoa agri‐food chain: transport of the cocoa harvest, classification, fermentation, drying, storage, and commercialization. Our methodology includes a modeling scheme combining optimization and simulation models, considering variability in the processes, and covering operational (transport and resource allocation), tactical (design and sizing of the processing plant), and strategic (sales dynamics) decisions across the cocoa value chain. We illustrate this methodology in a case study in Arauca, Colombia. Our findings emphasize the importance of combining these operational and strategic models since their inputs and outputs are interconnected influencing the decision‐making within the cocoa value chain. Our study also identifies key determinants for the postharvest design, highlighting the postharvest center capacity, FFC prices, and the market selling mode (export or local).