Cocoa (Theobroma cacao L.), one of the most important agricultural commodity products, is the key raw material for chocolate manufacturing. It is a source naturally occurring polyphenolic compounds and have been widely studied for their beneficial effects to human health. The objective of this study was to evaluate the fermentation time required to obtain more bioactive compounds and higher antioxidant activity in order to propose a mixture of unfermented and fermented cocoa beans in varying concentrations. Samples were collected every 12 h over a fermentation period of 144 h and evaluated according to their physico-chemical characteristics, as well as the content of bioactive compounds. It was verified that after 48 h of fermentation occurred a significant reduction in slate seeds, the appearance of partially fermented beans and the elevation of acidity and temperature. Until this period, a higher content of bioactive compounds with antioxidant activity was also observed. Thus, it is possible to propose a blend of cocoa beans fermented for 48 h and completely fermented beans to elaborate functional chocolates.