Several studies have highlighted the particular vulnerability of the Mediterranean region regarding climate change. In Tunisia, predictions indicate a temperature increase of 2.7 °C on the horizon of 2050, which may contribute to the degradation of agro-ecosystems and particularly the olive sector. The question that arise: how will the “Zelmati” olive tree behaves in the case of global warming as it is predicted for the south of the country? Therefore, olive trees (Olea europaea L. cv. Zelmati) were cultivated in Kebili-Rjim Maatoug region, which is a desert oasis in southwestern Tunisia characterized by a hot desert climate. The physio-biochemical responses of olive trees as well as olive oil quality characteristics were determined in comparison to those of plants cultivated in the classic region of Sfax-Taoues characterized by an arid climate. Kebili-Rjim Maatoug region exhibited high temperature and insolation, low air humidity and rainfall than Sfax-Taoues region during the different phenological stages of the olive trees. The hot desert climate resulted in a decrease of chlorophyll content, associated with an increase of malondialdehyde, soluble proteins, proline and soluble sugars contents in leaf tissues. Furthermore, polyphenols and carotenoids contents significantly increased (p < 0.05) in olive oil from olive trees grown in Kebili-Rjim Maatoug region. Nevertheless, the oleic acid content decreased below 50%, the palmitic acid exceeded 20% and the linolenic acid exceeded 1%, which was not in accordance with the commercial standards of olive oils.