The intestinal microbiome plays an important role in the metabolism of chemical compounds found within food. Bacterial metabolites are different from those that can be generated by human enzymes because bacterial processes occur under anaerobic conditions and are based mainly on reactions of reduction and/or hydrolysis. In most cases, bacterial metabolism reduces the activity of dietary compounds; however, sometimes a specific product of bacterial transformation exhibits enhanced properties. Studies on the metabolism of polyphenols by the intestinal microbiota are crucial for understanding the role of these compounds and their impact on our health. This review article presents possible pathways of polyphenol metabolism by intestinal bacteria and describes the diet-derived bioactive metabolites produced by gut microbiota, with a particular emphasis on polyphenols and their potential impact on human health. Because the etiology of many diseases is largely correlated with the intestinal microbiome, a balance between the host immune system and the commensal gut microbiota is crucial for maintaining health. Diet-related and age-related changes in the human intestinal microbiome and their consequences are summarized in the paper.