Ecuador is one of the main cocoa exporters in Latin America and the top producer of high-quality fine cocoa (~ 65%) in the world. However, there is a lack of knowledge regarding the physicochemical properties of cacao grown locally in the Ecuadorian Amazon region, since these properties have seldom been studied. In addition, it is necessary to improve the postharvest process adapted to the environmental conditions of the Amazon region. This study evaluated the effect of a semi-automatic fermentation system on the main physical and chemical characteristics [weight of 100 beans, cotyledon pH, fermentation percentage, total fat content, and total polyphenol content (TPC)] of Theobroma cacao L. (Nacional and Super Árbol). A full factorial design 22 was used to determine the influence of the factors studied: genotype and fermentation method (semi-automatic and Rohan boxes). The influence of the fermentation method had a highly significant (p < 0.05) positive effect, while the variety of cocoa did not significantly influence the fermentation percentage (p > 0.05). The cocoa beans fermented by the semi-automatic method met the quality parameters for fine aroma cocoa according to the Ecuadorian standard. This method achieved a 10% reduction in fermentation time compared to the traditional system (Rohan boxes). The values obtained for the cotyledon pH (5.85) and TPC (52.8 mg GAE/g) stand out as being directly related to the organoleptic characteristics of chocolate and its derivatives. This indicates that the semi-automatic method can be applied to both cocoa genotypes.