Penicillium digitatum is one of the most important causes of postharvest decay of Mexican lime fruit. The first stage of this study dealt with examining the effect of savory (Satureja hortensis) essential oil on P. digitatum mycelial growth in vitro. Savory essential oil (SEO) applied at concentrations of 0, 200, 400, 600, 800, 1000, and 1200 μL·L−1 to potato dextrose agar (PDA) medium. The results revealed that the application of SEO at concentrations of 1000 and 1200 μL·L−1 completely prevented the growth of P. digitatum. Gas chromatography–mass spectrometry results indicated that the dominant components of SEO were carvacrol (55.67%) and γ-terpinene (31.98%). In the second phase of the experiment, in vivo assays were conducted to evaluate the efficiency of SEO (800 and 1000 μL·L−1), hot water (40 and 50 °C), and gum arabic coating (2.5% and 5%) in restricting the fungi activity on Mexican lime fruit. The Mexican lime fruit were immersed in the aqueous solutions of SEO and gum arabic or in the hot water for 5 minutes, and then stored at 8 °C for 30 days. Savory essential oil at the concentration of 800 μL·L−1 proved to be the most effective treatment in conserving bioactive compounds of the fruits such as total phenols. This treatment also optimally maintained antioxidant activity and suppressed the activity of polyphenol oxidase (PPO) in the fruit peel. Moreover, hot water at 40 °C caused the least physicochemical changes and the highest appearance quality during storage.