Chocolate is a widely consumed product worldwide due to its exquisite flavor, which comes from the unique and fascinating cocoa flavor. This flavor depends on little controllable variables such as the genotype and the agroecological niche, and on the other side, on postharvest operations: (1) cocoa transformation from seeds to beans that comprises cocoa seeds preconditioning, fermentation, and drying, and (2) the production of chocolate from the bean in which roasting is highlighted. Postharvest transformation operations are critically important because during these, cocoa flavor is formed, allowing the differentiation of two categories: bulk and specialty cocoa. In this sense, this article presents an overview of cocoa postharvest operations, the variables and phenomena that influence and control the physical and biochemical transformation from seeds to cocoa beans, and their relation to the formation of chocolate flavor. Moreover, research perspectives in terms of control and management of postharvest practices in order to obtain cocoa with differentiated and specialty characteristics "from bean to bar" are discussed.