Both the peach fruit fly, Bactrocera zonata (Saunders), and the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), attack a wide variety of tree fruits worldwide. Exporting fruit hosts of these pests from countries where they are endemic to those where they are absent but may spread requires phytosanitary treatments. This research is to determine if C. capitata and B. zonata could be phytosanitary controlled by ozone treatment schedules. Moreover, elucidates the efficiency of ozone application in controlling microbial growth during the storage of fruits under cooling. Existing results proved that exposing infested fruits (guava and mandarin) with tephritids (C. capitata and B. zonata) to ozone gas for a time reaching 8 hours is sufficient for getting rid of immature stages (eggs, 1^st, 2^nd, and 3^rd larval instars) inside fruits. On the other hand, the results indicated that the ozonation process at 1000 ppm for 6 and 8 hours reduced the total fungal count (TFC) compared to the control samples. Ozone application may be an effective strategy for guava and mandarin fruits to retain post-harvest quality and have a longer period of storage, even though ozone-treated fruits have increased ascorbic acid levels.