Cocoa beans from different geographical and genetic origins show distinct fermentation dynamics which result in different chocolate qualities. In order to understand the effects of genetic improvement of cocoa plants, in this work volatile compounds and proteins profiles of beginning and end of the fermentation from different cocoa hybrids (CEPEC2004, PH15, PS1319, SJ02) were searched. Moreover, sensorial characterization of the produced chocolate from these hybrids was performed. According to the results obtained, different volatile compounds were identified in fermented beans and in the chocolate produced. Chocolate from CEPEC2004 was the most accepted by judges and correlated with sweet and bitter taste which can be explained by the presence of desired flavor compounds, such as 2,3-butanediol and 2-methyl-1-butanol. A higher presence of acids (undesirable compounds) was observed in chocolates samples from PS1319 hybrid, that have resulted in the low acceptance by judges. In addition, MALDI-TOF MS analysis showed that during fermentation the protein profile was different among the hybrids, which indicates this kind of compounds also contributes to the cocoa-specific flavor.