A significant increase in interest in new, naturally occurring sources of antioxidants is evident not only in the food industry but also in the pharmaceutical and cosmetic industries. Plant sources such as fruits, both traditional and less common, are often investigated. Goji berries (Lycium barbarum, Lycium chinense, and Lycium ruthenicum) represent fruits rich in polyphenols, especially phenolic acids (38.91 to 455.57 mg/kg FW) and flavonoids, with black goji berries (L. ruthenicum) containing a predominance of anthocyanins (119.60 to 1112.25 mg/kg FW). In this review, a comparison of polyphenol occurrence and content in the orange-red and black berries of L. barbarum, L. chinense, and L. ruthenicum is described. Goji berries represent a valuable source of nutrients and bioactive compounds that manifest a wide range of health-promoting effects. These benefits represent antioxidant, neuroprotective, and cytoprotective impacts, with effects on the metabolic control of glucose and lipids. This review is focused on an overview of the polyphenolic compounds occurring in these fruits, as well as their antioxidant activity and health benefits.