During fermentation, ethanol and acetic acid diffuse into the beans and, combined with the increased temperature, kill the seed embryo; consequently, the internal structure of the cocoa bean breaks down, releasing compounds and pigments that interact biochemically with activated endogenous hydrolases to develop flavor and color precursors (Afoakwa et al., 2008 and Schwan and Wheals, 2004). This study investigated the microbial communities and the physicochemical changes inside and outside of cocoa beans during the spontaneous fermentation of the three cocoa hybrids cultivated in Brazil.