Flavonoids protect plants against various biotic and abiotic stresses, and their occurrence in human diet participates in preventing degenerative diseases. Many of the biological roles of flavonoids are attributed to their potential cytotoxicity and antioxidant abilities. Flavonoid oxidation contributes to these chemical and biological properties and can lead to the formation of brown pigments in plant tissues as well as plant-derived foods and beverages. Flavonoid oxidation in planta is mainly catalyzed by polyphenol oxidases (catechol oxidases and laccases) and peroxidases. These activities are induced during seed and plant development, and by environmental stresses such as pathogen attacks. Their complex mode of action is regulated at several levels, involving transcriptional to post-translational mechanisms together with the differential subcellular compartmentalization of enzymes and substrates.