The current scientific knowledge on the relationship between diet and human health is greatly focused on the effects of phytochemicals, especially polyphenols, on chronic diseases, due to their preventive effect as shown by many epidemiological studies. Herbs, cocoa products, and darkly colored berries, such as black elderberries, chokeberries, and black currants, are the richest dietary sources that contribute to the average intake of polyphenols of about 1 g/day. Polyphenols that are the most common in the human diet are not necessarily the most active in the body because their beneficial effects depend on the plant matrix in which they are incorporated and on processing methods and endogenous factors such as microbiota and digestive enzymes. Polyphenol-rich foods are considered as being potential functional foods due to antioxidant, anti-inflammatory, antimicrobial, immunomodulatory, anticancer, vasodilating, and prebiotic-like properties. This review will outline findings on the preventive effects of polyphenols on chronic diseases, the factors affecting polyphenol bioavailability and bioaccessibility, and new trends in functional food production.