A growing body of literature is available about the valorization of food by-products to produce functional foods that combine the basic nutritional impact with the improvement of the health status of consumers. In this context, this study had two main objectives: (i) An innovative multistep extraction process for the production of a refined olive oil enriched with phenolic compounds (PE-ROO) extracted from olive pomace, olive leaves, or grape marc was presented and discussed. (ii) The most promising PE-ROOs were selected and utilized in in vitro and in vivo trials in order to determine their effectiveness in the management of high fat diet-induced-metabolic syndrome and oxidative stress in rats. The best results were obtained when olive leaves were used as source of phenols, regardless of the chemical composition of the solvent utilized for the extraction. Furthermore, while ethanol/hexane mixture was confirmed as a good solvent for the extraction of phenols compounds soluble in oil, the mix ROO/ethanol also showed a good extracting power from olive leaves. Besides, the ROO enriched with phenols extracted from olive leaves revealed an interesting beneficial effect to counteract high fat diet-induced-metabolic disorder and oxidative stress in rats, closely followed by ROO enriched by utilizing grape marc.