The flavoring of olive oils with aromatic plants is commonly used to enrich the oils with aromatic and antioxidant compounds. Origanum majorana L. was applied as a flavoring agent for extra virgin olive oil (EVOO), at concentrations of 20 g L−1 and 40 g L−1, via ultrasound-assisted maceration. The aim of this study was to evaluate the impact of flavoring on the EVOOs’ quality indices, oxidative stability, and antioxidant, antiradical and antifungal activities, as well as on the oils’ volatile and phenolic profile. The flavored EVOO maintained the quality indices (free fatty acids, peroxide value, extinction coefficients) below the maximum permitted levels, whereas the addition of marjoram enhanced the oxidative stability, the levels of chlorophyll and b-carotene and the total phenolic content. The incorporation of marjoram into the EVOO did not have a significant impact on the antioxidant and antiradical activities. Concerning the antifungal activity, no Zygosaccharomyces bailli cell growth was observed for two weeks in a mayonnaise prepared with the flavored EVOO at a 40 g L−1 concentration. SPME-GC-MS analysis revealed the presence of 11 terpene compounds (hydrocarbon and oxygenated monoterpenes) that had migrated from marjoram in the flavored EVOO. Twenty-one phenolic compounds were tentatively characterized by LC-QToF-MS in the EVOO samples; however, hesperetin and p-coumaric acid, originating from marjoram, were only detected in the flavored EVOO.