In order to address the issue of the lotus root's challenging washing process and the remnant of contaminants such as sludge and microorganisms during washing, this study evaluates the effect of an innovative washing method of ultrasonic combined bubbling-assisted low-concentration peroxyacetic acid (PAA) on the washing of lotus root. Single/multifrequency ultrasound, PAA concentration, washing time, and process combination sequence of soaking, ultrasound, and bubbling were explored. Moreover, the effects on the physicochemical quality of lotus root and the decontamination mechanism under this washing method were analyzed. The results showed that soaking before both ultrasonic and bubbling washing was effective in reducing surface microorganisms. Decontamination with 0.04% PAA can effectively sterilize more than 90% of all bacteria. Combination of bubbling, low concentration of PAA soaking, and ultrasonic washing of lotus root was the most effective (sterilizing and decontaminating). The ultrasonic treatment increased the total phenolic content (TPC) of lotus root by 16.4% and antioxidant activity (DPPH, FRAP) by 13.5% and 28.7%, whereas PAA was detrimental to the retention of TPC and antioxidant active compounds in lotus root. Furthermore, the combination of ultrasound and PAA produced greater damage to bacterial cell membranes and better bactericidal effects.