Olive oil is famous due to the nutritional properties and beneficial health effects. The exceptional properties of virgin (VOO) and extra virgin olive oil (EVOO) are credited to the bioactive constituents of their polar fraction, the phenolic compounds. The concentration and composition of biophenols can be influenced by the geographical origin, the cultivar, as well as several agronomic and technological parameters. In this study, an ultra-high-performance liquid chromatography coupled to quadrupole-time of flight tandem mass spectrometry (UHPLC-QTOF-MS) method was used to determine biophenols in Greek EVOOs from five islands originating from the North Aegean Region (Chios, Fournoi, Ikaria, Lesvos, and Samos) through target and suspect screening. In total, 14 suspect and 5 target compounds were determined in the analyzed EVOOs. The quantitative and semiquantitative results were compared to investigate discriminations between different regions. Significant differences were found between the islands based on the overall phenolic content and the concentration levels of individual compounds, as well. In the case of Lesvos, the territory was separated in subdivisions (zones), and each zone was studied individually.