The present invention relates to a process of obtaining a natural, bioactive concentrate, rich on hydroxytyrosol, from olive tree residues and subproducts using clean technologies. These technologies comprise supercritical fluid extraction, nanofiltration and reverse osmosis which are used individually or in an integrated mode. The natural extract comprises a minimum concentration of 15% (mass fraction) in hydroxytirosol and a maximum concentration of 98% (mass fraction) in this compound. The hydroxytyrosol-rich concentrate exhibits anti-oxidant, anti-microbial, anti-inflammatory and anti-carcinogenic activities, which are superior to the activities observed for isolated hydroxytyrosol in equivalent concentration. The hydroxytyrosol-rich concentrate can be prepared in the form of solid particles, as an aqueous solution, in an emulsion or as lipidic based nanoparticles. Industrial application comprises the food, pharmaceutical and cosmetics industries.