This study was designed to examine the effect of thermal treatment at different temperatures (70, 90 and 110 °C) over time (0–120 min) on the phenolic content and antioxidant activity of Myrtus communis L. ethanol extract in acetate buffer (pH = 3). Total phenols, flavonoids and proanthocyanidins contents and the radical scavenging activity, monitored during the treatment, were significantly influenced by the applied temperature (p < 0.05). The higher the temperature and the duration of the treatment, the greater the degradation and the loss of these compounds. Likewise, DPPH⋅ radical scavenging activity decreased, in a temperature-depending manner, during thermal treatment. Nonetheless, the results of the ABTS⋅+ test showed that the activity remained almost stable during the treatment. Furthermore, the kinetics of degradation of compounds analysed by HPLC-DAD, namely myricetin-3-O-galactoside, quercetin-3-O-glucoside and quercetin-3-O-rhamnoside was investigated and their energy of activation was determined. Degradation rate in case of quercetin-3-O-rhamnoside was the most sensitive to temperature (20.536 kJ/mol) followed by myricetin-3-O-galactoside (12.268 kJ/mol) and quercetin-3-O-glucoside (2.838 kJ/mol). The use of the discriminant analysis has shown that some other factors other than temperature and time of thermal treatment might also have a minor influence on the content of total phenolics, total flavonoids, proanthocyanidins and values of the antioxidant tests (DPPH⋅, ABTS⋅+) in the investigated extracts of M. communis L.