The phenolic profiles of three typical Tuscan olive cultivars, Frantoio, Moraiolo and Leccino, stored in different conditions (fresh, frozen and whole lyophilized fruits), have been compared during the ripening period. Our main goals were to evaluate the phenolic content of whole freeze-dried fruits and to test the stability of the corresponding cake in oxidative-stress conditions. The comparison of fresh and whole freeze-dried fruits from the 2012 season gave unexpected results, e.g. oleuropein in lyophilized fruits was up to twenty times higher than in fresh olives with values up to 80.3 g/kg. Over time we noted that the olive pastes obtained from lyophilized olives contained highly stable phenolic compounds, even under strong oxidative stress conditions. Finally, it was also observed that the cake/powder obtained from unripe freeze-dried olives was very poor in oil content, and therefore quite suitable for use in nutritional supplements rich in phenolic compounds, such as secoiridoids which are not widely present in the human diet.