Tomato is perishable and requires preservation to extend its shelf life. In this study, we conducted selection processes to identify essential oils that can help to avoid spoilage and deterioration during tomato storage and extend the shelf life. Thereafter, we determined the phosphatase activity assay, potassium ion concentration, and electron microscopy to study the antibacterial mechanism of essential oil. We found that Enterobacter ludwigii W01 was the dominant spoilage bacterium in tomatoes with cracked and curled skin. We selected oregano essential oil from 12 essential oils (oregano essential oil, lemon essential oil, osmanthus essential oil, cypress wood essential oil, tea tree essential oil, licorice essential oil, Baili essential oil, white camphor essential oil, Shancang seed essential oil, rosemary essential oil, rose essential oil, and cinnamon essential oil) which could significantly inhibit the activity of E. ludwigii W01. However, the diameter of the inhibition zone for Wh, Te, Cy, Li, Rm, Le, and Os is 0 mm, the diameter of the inhibition zone for Ba, Sh, and Ro was less than 1.0 mm, whereas the diameter of the inhibition zone for Ci and Or was greater than 2.0 mm. The diameter of the suppression circle for Ci and Or was greater than 2.0 mm, while Ci was lesser than Or. Oregano essential oil can damage the cell wall of E. ludwigii W01, leading to the leakage of the alkaline phosphatase stored between the cell wall and the cell membrane which can increase the alkaline phosphatase activity in the bacterial solution. Meanwhile, the addition of oregano essential oil significantly altered the cellular morphology of E. ludwigii W01. Spraying the surface of fresh tomato fruits with 1 MIC (0.125%) of oregano essential oil prolonged the storage time to 15 days, without significant changes in its sensory attributes. Those results indicated that oregano essential oil was a potential preservative for tomatoes.
