The flavor and aroma of cacao (Theobroma cacao) beans were the main reasons that promoted its domestication and food-use by pre-Columbian peoples of Mesoamerica. Polyphenols and alkaloids are compounds that directly affect the flavor of the cocoa beans and indirectly on the flavor precursors. The alkaloids are associated with bitterness; its concentration is related to the cultivar and its modifying through the processing. Polyphenols molecules are responsible together with other molecules of the astringency (not desirable in chocolate), but also are responsible for antioxidant properties, very desirable by consumers. This review focuses on aspects of the biosynthesis of these important molecules in cocoa beans as well as implications in taste and flavor. The changes of these molecules that occur during processing are also approached.