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In this study, an overall survey regarding the determination of several bioactive compounds in olive fruit is presented. Two methodologies were developed, one UPLC-Q-TOF-MS method for the determination of olive fruit phenolic compounds and one HPLC-DAD methodology targeting the determination of pigments (chlorophylls and carotenoids), tocopherols (α-, β, -γ, δ-) and squalene. Target and suspect screening workflows were developed for the thorough fingerprinting of the phenolic fraction of olives. Both methods were validated, presenting excellent performance characteristics, and can be used as reliable tools for the monitoring of bioactive compounds in olive fruit samples. The developed methodologies were utilized to chemical characterize the fruits of the Kolovi olive variety, originating from the island of Lesvos, North Aegean Region, Greece. Twenty-five phenolic compounds were identified and quantified in Kolovi olives with verbascoside, hydroxytyrosol, oleacein and oleomissional found in significantly high concentrations. Moreover, 12 new bioactive compounds were identified in the samples using an in-house suspect database. The results of pigments analysis suggested that Kolovi variety should be characterized as low pigmentation, while the tocopherol and squalene content was relatively high compared to other olive varieties. The characterization of Kolovi olive bioactive content highlighted the high nutritional and possible economic value of the Kolovi olive fruit.