Beer is the most widely consumed fermented beverage in the world. A moderate consumption of beer has been related to important healthy outcomes, although the mechanisms have not been fully understood. Beer contains only a few raw ingredients but transformations that occur during the brewing process turn beer into a beverage that is enriched in micronutrients. Beer also contains an important number of phenolic compounds and it could be considered to be a source of dietary polyphenols. On the other hand, gut microbiota is now attracting special attention due to its metabolic effects and as because polyphenols are known to interact with gut microbiota. Among others, ferulic acid, xanthohumol, catechins, epicatechins, proanthocyanidins, quercetin, and rutin are some of the beer polyphenols that have been related to microbiota. However, scarce literature exists about the effects of moderate beer consumption on gut microbiota. In this review, we focus on the relationship between beer polyphenols and gut microbiota, with special emphasis on the health outcomes.