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The productiveness of ultrasound (US) is affected by its frequency, power, and time, which has been reported to be very effective during food treatment when combined with other techniques of treatments. The study was aimed to evaluate the effect of mono‐frequency (MFU), simultaneous dual‐frequency (SDFU), and simultaneous tri‐frequency US (STFU) at treatment times of 5–25 min on microbial inactivation and nutritional quality of cherry tomato. Results revealed that within 10 min of sonication, SDFU was most effective compared with MFU toward inhibiting the spoilage microorganisms, delaying ripening as well as maintaining firmness, total phenolic, flavonoid, and antioxidant of the fruit during 21 days of storage at 4°C. Although STFU caused a higher reduction in microbial load after treatment, it, however, showed several adverse effects on the fruit during storage. Overall, SDFU treatment had great potential …