Oleuropein (OE) is a secoiridoid glycoside occurring mostly in the Oleaceae family and presenting several pharmacological properties, including hypolipidemic and antioxidant properties. Based on these, several dietary supplements containing olive leaf extracts enriched with OE are commercially available in many countries. The current study aimed to examine the effect of supplementation with such an extract on the serum and urine metabolome of young healthy male athletes. For this purpose, applying a randomized, balanced, double-blind study, nine young, healthy males (physical education students) received either a commercially prepared extract or placebo for one week, followed by a two-week washout period; then, they were subsequently dosed with the alternate scheme (crossover design). Urine and serum samples were analyzed using UHPLC-HRMS, followed by evaluation with several multivariate methods of data analysis. The data were interpreted using a multilevel metabolomic approach (multilevel-sPLSDA) as it was found to be the most efficient approach for the study design. Metabolic pathway analysis of the most affected metabolites revealed that tryptophan and acylcarnitine's biochemistries were most influenced. Furthermore, several metabolites connected to indole metabolism were detected, which may indicate enhanced serotonin turnover. Phenylethylamine and related metabolites, as well as estrone, were connected to enhanced performance. In addition, possible changes to the lipidemic profile and the blood and urine redox statuses were investigated.