Cocoa tree plantations aim to harvest grains found in the cob to produce cocoa and chocolate. There has been a growing interest in valorizing the secondary components of the cocoa fruit, such as the peel, placenta, and mucilage/pulp, as valuable sources of nutrients for healthy food preparation. In other words, by-products derived from these raw materials are an exploitable source of nutrients in the preparation of healthy food. In the present study, two varieties of cocoa, National Cocoa Fino de Aroma (NCFA) and Colección Castro Naranjal 51 (CCN-51), were evaluated and harvested during both dry and rainy seasons. This evaluation was based on the profiling of the cob, peel, grain, placenta, and mucilage in different stages of ripeness (underripe, ripe, and overripe). Also, from the ripe raw material, a fermented beverage prototype was developed, such as kombucha, with different concentrations of mucilage (40, 60, 80, and 100 g/L). Physicochemical analyses, such as acidity, ◦Brix, pH, moisture, ash, protein, fat, fiber, vitamins, sugars, and polyphenols of the raw mucilage material and acidity, ◦Brix, and pH values of the fermented kombucha, were carried out. The best performances were obtained with the CCN-51 variety in the rainy season. Among the fermented drink panelists, the CN40 treatment (Nacional Mucilage + 40 g/L of sugar) received the highest acceptability and was considered the best. Given its efficiency, nutritional content, and potential applications, this product presents a promising strategy to address Sustainable Development Goals related to zero hunger, health and well-being, and climate action.