Polyphenols can be considered the largest group of natural antioxidants, which includes flavonoids, hydrolysable and condensed tannins, phenolic acids, stilbenes, lignans, and phenolic aldehydes. All these compounds have potential health-promoting properties such as increasing peripheral blood flow and possess antioxidant, anticancer, anti-cardiovascular, and other anti-degenerative properties. The use of polyphenols in food is a convenient and viable approach to increase their daily intake. Out of the whole polyphenol intake, it is the action of gut bacteria that will further modulate and affect polyphenol bioaccessibility. In addition, phenolic compounds can modulate the gut microbiota into a healthier community. Studies indicate that some phenolic compounds have low absorption at small intestinal level with a large amount reaching the colon to be then metabolized by the local microbiota. This microbial transformation produces smaller and more absorbable compounds, named metabolites with potential bioactivity. This chapter will discuss the influence of polyphenols on human microbiota, the microbial role on the transformation of phenolic compounds, the health benefits of the formed metabolites and point out how those compounds can be found for ingestion.