The European Food Safety Authority highlights the beneficial effects of olive oil phenols, mainly, secoiridoids. Nevertheless, the metabolism of secoiridoids in humans has not been fully elucidated. This research evaluated the metabolism of secoiridoids in humans after intake of olive oils with diverse phenolic profiles. For this purpose, three extra virgin olive oils (EVOOs) were ingested by six volunteers at scheduled meals, and urine samples were collected the following morning for subsequent LC-MS/MS analysis. Using untargeted analysis, urinary metabolites revealed representative patterns associated with the various olive oil phenolic contents in absolute and relative terms. We were able to identify metabolites obtained through phase I, phase II, and microbial metabolism with discrimination between tyrosol and hydroxytyrosol derivatives. Metabolism of phenols is differentially activated as a function of the olive oil secoiridoids content, and this proof-of-concept study shows how urinary metabolites represent olive oil phenolic content.