The health benefits of extra virgin olive oil (EVOO) are related to its chemical composition and the presence of bioactive compounds with antioxidant properties. The aim of this study was to evaluate antioxidant compounds (pigments, coenzyme Q10 (CoQ10) and phenolic compounds) and antioxidant properties of EVOO from the same region comparing different cultivars (Hojiblanca and Arbequina), harvest year and crop stage. Antioxidant properties of oils were studied before and after a gastrointestinal digestion process, by in vitro assays (DPPH, ABTS and FRAP) and antioxidant markers in Caco-2 cells (reactive oxygen species production). The content of bioactive compounds measured was significantly affected by cultivar and harvest year (except for carotenoids) and by the crop stage (except for coenzyme Q10). Higher amounts of coenzyme Q10 were observed in Hojiblanca than in Arbequina EVOO. Total phenol content and antioxidant properties were also different depending on cultivar and harvest year and the in vitro digestion process strongly improved antioxidant marker values. Antioxidant potential in bioaccessible fractions was mainly related to the content of coenzyme Q10 and phenolic compounds in EVOO. Chemometric analysis showed that the oils were clearly classified by cultivars, harvest and crop stage, according to the chemical composition and antioxidant activity analyzed in the present study.