The role of gut microbiota in human health has been investigated extensively in recent years. The association of dysbiosis, detrimental changes in the colonic population, with several health conditions has led to the development of pro-, pre- and symbiotic foods. If not absorbed in the small intestine or secreted in bile, polyphenols and other food components can reach the large intestine where they are susceptible to modification by the microbial population, resulting in molecules with potentially beneficial health effects. This review provides an overview of studies that have detected and/or quantified microbial phenolic metabolites using high-performance liquid chromatography as the separation technique, followed by detection through mass spectrometry. Both in vitro experimental studies and human clinical trials are covered. Although many of the microbial phenolic metabolites (MPM) reported in in vitro studies were identified in human samples, further research is needed to associate them with clinical health outcomes.