(Poly)phenols (PPs) constitute a large family of phytochemicals with high chemical diversity that are known to be active principles of plant-derived nutraceuticals and herbal medicinal products. Their pharmacological activity, however, is difficult to demonstrate due to their mild physiological effects, and to the large inter-individual variability observed. Many PPs have little bioavailability and reach the colon almost unaltered. There they encounter the gut microbes resulting in a two-way interaction in which PPs modulate the gut microbiota composition, and the intestinal microbes catabolize the ingested PPs to release metabolites that are often more active and better absorbed than the native phenolic compounds. The type and quantity of the PP metabolites produced in humans depend on the gut microbiota composition and function, and different metabotypes have been identified. However, not all the metabolites have the same biological activity, and therefore the final health effects of dietary PPs depend on the gut microbiota composition. Stratification in clinical trials according to individuals’ metabotypes is necessary to fully understand the health effects of PPs. In this review, we present and discuss the most significant and updated knowledge regarding the reciprocal interrelation of the gut microbiota with dietary PPs as a key factor that modulates the health effects of these compounds. The review will focus in those PPs that are known to be metabolized by gut microbiota resulting in bioactive metabolites.