The comprehensive phenolic fingerprints of flowers, peels and leaves of two Tunisian L. cultivars, namely Nabli and Gabsi, were investigated. The highest phenolic content was recorded in the Nabli flowers, followed by Gabsi peels extracts (152.6 and 125.8 mg gallic acid equivalent 100 g, respectively) while flavonoids and flavonols were highest in Gabsi peels (19.2 and 26.0 mg Rutin equivalent per 100 g). Besides, the antioxidant capacity was the highest in Gabsi peels (144.4 mg gallic acid equivalent 100 g) and in Nabli flowers (161.6 mg gallic acid equivalent per 100 g. Methanol extracts of all three plant portions of both cultivars were screened by ultra-high-performance liquid chromatography coupled to quadruple time of flight mass spectrometry, and the identified phenolics were further quantified. Nabli cultivar showed higher contents of flavonoids (in flowers and leaves), while phenolic acids were abundant in Gabsi leaves. Multivariate statistics highlighted differences in phenolic profile among organs and cultivars. These results showed that the pomegranate portions investigated are a valuable source of bioactive compounds with health-promoting properties, mainly belonging to the phenolic class of flavonoids.