A characterization of the phenolic profile of 25 cocoa genotypes established in a Mexican gene bank was carried out. From five different extraction methods commonly used for phenols, extraction with acidified methanol-water was chosen as the best to quantify the concentrations of theobromine and individual phenols in cocoa beans. High concentrations of individual and total phenols were found for genotypes native to Mexico (like RIM105, M031, and M033) or from Peru and Ecuador (INI10), but not the commercial mix (CAF), and were directly associated with their antioxidant activities. Despite the loss of some theobromine and phenols during fermentation, epicatechin remained in the fermented cotyledon in high concentrations. This study could help promote the commercialization of Mexican genotypes of cocoa and reports the possibility of upcycling fermented cocoa husks, which are rich in bioactive compounds and fiber, as novel functional extracts for use in food formulation or for nutraceutical purposes.