Quercetin is one of the main dietary flavonols, but its beneficial properties in disease prevention may be limited due to its scarce bioavailability. For this purpose, delivery systems have been designed to enhance both stability and bioavailability of bioactive compounds. This study aimed at investigating the human microbial metabolism of quercetin derived from unformulated and phytosome-formulated quercetin through an in vitro model. Both ingredients were firstly characterized for their profile in native (poly)phenols, and then fermented with human fecal microbiota for 24 h. Quantification of microbial metabolites was performed by ultra-high performance liquid chromatography coupled to mass spectrometry (uHPLC-MSn) analyses. Native quercetin, the main compound in both products, appeared less prone to microbial degradation in the phytosome-formulated version compared to the unformulated one during fecal incubation. Quercetin of both products was bioaccessible to colonic microbiota, resulting in the production of phenylpropanoic acid, phenylacetic acid and benzoic acid derivatives. The extent of the microbial metabolism of quercetin was higher in the unformulated ingredient, in a time-dependent manner. This study opened new perspectives to investigate the role of delivery systems on influencing the microbial metabolism of flavonols in the colonic environment, a pivotal step in the presumed bioactivity associated to their intake.