Activity of the polyphenol oxidase (PPO) from eggplant fruit (Solanum melongena L.) on phenolic compounds of an extra virgin olive oil (EVOO) was studied. In standardized reaction solutions, the eggplant PPO, isolated in the laboratory, depleted completely chlorogenic and caffeic acids, oleuropein, and verbascoside, while the levels of hydroxytyrosol reduced by half. Conversely, no activity of the PPO was observed on the gallic and protocatechuic acids nor on mono-phenols, such as tyrosol and the p-coumaric, o-coumaric, and ferulic acids. PPO activity on phenols extracted from eggplant fruit and EVOO confirmed the enzyme substrate specificity and caused a significant decrease in the measure of total phenols and o-diphenols. Similarly, PPO crude extract caused a significant decrease of polyphenols directly in the EVOO. Moreover, maximum degradation of EVOO polyphenols was observed when olive oil was homogenized with eggplant fruit pulp to form a cream-like puree. In fact, immediately after the preparation, total phenols and o-diphenols of the olive oil recovered from the eggplant-oil puree were decreased by similar to 80% and 100% compared to those of the initial EVOO. As a consequence, the oxidative stability of the recovered oil was similar to 60% lower than that of the initial EVOO. In conclusion, in the preparation of vegetable preserves, a residual activity of phenol oxidase may adversely affect the quality and shelf life of the extra virgin olive oil used as covering.