Cocoa is rich in phytochemicals. In unfermented cocoa beans, pigment cells make up about 11%-13% of the tissue. The pigment cells contain approximately 65%-70% polyphenols and 3% anthocyanins by weight. During fermentation the polyphenols undergo a variety of reactions, including self-condensation and reaction with proteins and peptides. Approximately 20% of the polyphenols (by weight) remain at the end of the fermentation process. Roasting and other cocoa processing activities also cause changes. The level of polyphenols will vary with the variety of cocoa bean and with the degree of fermentation.

A study found that the main phytochemicals and polyphenolics found in cocoa are:

Another study reported that the total polyphenol content of the bean is estimated to be 6% to 8% by weight of the dry bean.

The catechins are colourless, while the anthocyanins give rise to the purple colour of unfermented beans. During fermentation and drying the anthocyanins are converted to quinonic compounds to give the bean its characteristic brown colour. One piece of research on the total amount of polyphenol in finished cocoa products, using the Folin-Ciocalteau analysis of organic solvent extracts, found 20,000ppm in cocoa powder, 8,400ppm in baker's chocolate and 5,000ppm in milk chocolate