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Mature fruits of Olea europaea L. ‘Frantoio’ with different degrees of damage [from 0% to 100% of fruits with exit holes (EHs)] caused by the olive fruit fly (Bactrocera oleae), the key pest in Mediterranean olive orchards, were sampled to quantify the effects on free acidity, peroxide value (PV), and concentrations of secoiridoids and lignans of virgin olive oil (VOO). The total concentration of phenolic compounds and that of individual secoiridoids were negatively related to the degree of fruit damage, whereas the concentration of lignans, namely (+)-pinoresinol and (+)-1-acetoxypinoresinol, was unaffected. Free acidity was similar for the 0% and 10% EH treatments, increased sharply between 10% and 30% EH, and was similar again for the 60% and 100% EH treatments. Free acidity values were low and well within the limit for VOO classification even after 6 months of oil storage. Peroxide value responded to both B. oleae damage and storage conditions. Peroxide values increased between 10% and 30% EH treatments but changed little between the 30% and 100% EH treatments regardless of oil storage conditions. Secoiridoid concentrations closely reflected the degree of B. oleae damage when sources of variability such as cultivar and cultural practices were kept under control and conditions of processing and oil storage were optimal.