Abstract Jaboticaba, a polyphenol-rich fruit, has numerous nutraceutical properties. Studies on jaboticaba composition have focused on solvent-extractable polyphenol compounds, whereas the matrix-bound polyphenols that can be delivered during digestion have been neglected. This study aimed to characterize the polyphenol profiling of matrix-bound and free phenolic compounds in Jaboticaba peel powder (JPP) using two fruit species, Myrciaria jaboticaba (JPP-MJ) and M. trunciflora (JPP-MT). An HPLC-DAD-MS/MS method was developed and validated to analyze JPP polyphenols. The total content of free phenolic compounds was 2.4 times higher in JPP-MT than in JPP-MJ and the profile of free polyphenols differed between the two species. JPP-MT had 60.3% tannins and 33% anthocyanins, whereas JPP-MJ had 34.7% and 50.7%, respectively. The content of matrix-bound phenolic compounds was higher in JPP-MJ than in JPP-MT (15.3% vs. 4.3% of total phenolic compounds). Besides cyanidin 3-glucoside, three other compounds were identified as major: a tetragalloylglucose isomer for both species, trigalloylglucose for JPP-MT, and delphinidin-3-glucoside for JPP-MT. Phenolic profiling of JPP revealed new compounds that may contribute to health benefits after JPP consumption. Despite differences in the phenolic profile between the jaboticaba species, both JPPs are rich sources of polyphenols and could be used for promoting health benefits.