This research focuses on the seasonal patterns of the ecophysiological recovery of four olive cultivars (Arbequina, Coratina, Frantoio, and Urano), both micropropagated and self-rooted, grown in a mature, irrigated, super high-density (SHD) orchard under Mediterranean conditions (Southern of Italy). The aim was to observe the impact of the micropropagation method on the ecophysiological responses. Ecophysiological parameters, including leaf water potential (LWP), stomatal conductance (gs), net photosynthetic rate (Pn), and transpiration rate (E) were assessed. Self-rooted trees consistently exhibited superior gs, E, and Pn recovery compared to the micropropagated ones. ‘Arbequina’ maintained elevated levels of Pn under water-deficit conditions. ‘Coratina’ exhibited increases in gs and E after irrigation. ‘Frantoio’ demonstrated recovery capabilities, with lower LWP and higher Pn under stress. ‘Urano’ micropropagated trees achieved higher gs values in mid-summer, while self-rooted trees sustained higher Pn later in the season. This field research highlighted the important role of the propagation method in optimizing the physiological performance of olive cultivars in SHD orchards. Furthermore, it highlighted the necessity of long-term studies on the effects of propagation methods and their interactions with other farming practices.