The purpose of this work was to evaluate some new filtration systems in relation to the quality of extra-virgin olive oil (EVOO). Filtration processes were undertaken using a polypropylene filter bag and two different inert gas flows as filter aids (argon and nitrogen). Qualitative and quantitative variations of the glyceride composition, antioxidant and pro-oxidant compounds, and water content were correlated with the oxidative stability to establish the effect on EVOO shelf life. The influence on physicochemical and sensorial properties was also evaluated. After filtration, the oxidative stability was reduced. The behavior of the polyphenols and water content on the filtration process could explain the lowest oxidative stability of filtered EVOO. Moreover, the results of the sensorial analysis confirmed that filtration using inert gases did not decrease the intensity of the main positive sensory attributes. The results could help olive-oil producers to improve EVOO quality and establish optimal storage conditions.