Theobroma cacao L. has been recognized for its many nutritional and health benefits since the Mayan and Aztec times. Linnaeus gave the name Theobroma to the fruits brought to Europe by Spanish sailors, which in Greek means “Food of the Gods.” Cocoa is one of the most important agricultural commodities and among the largest producers are Ghana, Ivory Coast, Nigeria, and Cameroon, followed by Brazil, Ecuador, and Indonesia. Theobroma cacao L. plays an important role in the food industry, cosmetic industry (for soaps, creams, and lotions), and other industrial applications for the production of juices, alcoholic beverages, jellies, and marmalades. In agriculture, it is used as an additive in animal food, as fertilizer, and as biodiesel. The polyphenols found in cocoa can be classified into two main groups—flavonoids and non-flavonoids. Methylxanthine alkaloids give cocoa its characteristic pungent and bitter taste. These bioactive compounds are extracted, purified, and identified, using both classical methods and the latest green techniques. Many researchers are working on beverages obtained from Theobroma cocoa L. In their reports, they prove the important antioxidant role played by the bioactive compounds in cocoa to improve the health of the human body and to protect it from various diseases such as cardiovascular, neurological, cancer, diabetes, and stress.