Araçá is a Brazilian native fruit belonging to the Myrtaceae family. Although some studies already prove its health benefits, it is still necessary to explore the phenolic compounds in all its parts separately. This study aimed to investigate the free, esterified, glycosylated, and insoluble phenolics in two morphotypes of araçá, red and yellow, evaluating peel, pulp, and seed separately, using liquid chromatography coupled to mass spectrometry (LC-ESI-QqQ-MS/MS). Fourteen phenolics and five anthocyanins were quantified in both morphotypes. The peels presented the highest contents, followed by the pulp and seeds. Red araçá stood out over the yellow one only in the phenolic fractions resulting from the peel, with the yellow araçá being superior in the phenolic fractions of the pulp and seed. The highest antioxidant capacities were detected for the pulp-esterified phenolics (498.3 µmol g⁻¹) and peel-free phenolics (446.7 µmol g⁻¹) of yellow araçá. Principal component analysis (PCA) indicated specific markers to differentiate the samples. All parts of the araçá proved to be a rich source of phenolic compounds, in different fractions, mainly in the peel. This information will be beneficial to stimulate the consumption of native fruits and their possible use in the development of new products.