Anthocyanins are naturally occurring compounds abundant in the human diet. Evidence has accumulated regarding the positive association of their intake with healthy biological effects. The microbiota has just been started to be considered as a metabolic organ, hence contributing to the metabolism of phenolic compounds and, consequently, to their bioavailability and the biological effects displayed by them. This review aimed to compile information regarding interaction of anthocyanins with the microbiota, from two perspectives: (i) identification of their colonic metabolites as potential bioactive molecules and (ii) their role as prebiotic agents. These perspectives are key points in anthocyanin metabolomics. Several metabolites have been identified after anthocyanin consumption with potential health benefits, in particular phenolic acids and simple phenols. On the other hand, microbiota modulation is closely related to several physiological impairments, and its modulation has been considered as a possible mechanism by which phenolic compounds may exert their effect.