The development of innovative technologies in the mechanical extraction process of extra virgin olive oil can improve its quality standards through the modulation of physical, chemical and biochemical processes. Extra virgin olive oil quality and varietal differentiation are influenced by many factors, particularly the extraction. The use of ultrasound technology in the extraction process does not affect the quality, the composition, and the thermal properties of the oil, facilitating its separation from solids, and it allows the release of active compounds from the olive paste, with a positive influence on the phenolic content. In this study, the impact of ultrasound technologies was evaluated on merceological parameters, quality profile, and organoleptic features of extra virgin olive oils extracted from whole and destoned olives of the three main Italian cultivars (i.e., Peranzana, Canino, and Coratina). The parameters analyzed were influenced by both genotype and treatment, in particular, sonication did not lead to significant changes in the nutraceutical profile of the oils. The de-stoned olives were able to determine a great improvement of oil quality both for phenolic and volatile composition with a significant enhancement of health and sensory properties of the product.