Berries are rich in phenolic compounds such as phenolic acids, flavonols and anthocyanins. These molecules are often reported as being responsible for the health effects attributed to berries. However, their poor bioavailability, mostly influenced by their complex chemical structures, raises the question of their actual direct impact on health. The products of their metabolization, however, may be the most bioactive compounds due to their ability to enter the blood circulation and reach the organs. The main site of metabolization of the complex polyphenols to smaller phenolic compounds is the gut through the action of microorganisms, and reciprocally polyphenols and their metabolites can also modulate the microbial populations. In healthy subjects, these modulations generally lead to an increase in Bifidobacterium, Lactobacillus and Akkermansia, therefore suggesting a prebiotic-like effect of the berries or their compounds. Finally, berries have been demonstrated to alleviate symptoms of gut inflammation through the modulation of pro-inflammatory cytokines and have chemopreventive effects towards colon cancer through the regulation of apoptosis, cell proliferation and angiogenesis. This review recapitulates the knowledge available on the interactions between berries polyphenols, gut microbiota and gut health and identifies knowledge gaps for future research.