Ultrasonic irradiation is one of the most promising membrane cleaning techniques for membrane bioreactors (MBRs) because of several advantages such as high flux-recovery capacity and in situ application without interrupting the filtration process. However, significant contradictions may be found and, consequently, this method has not yet been widely developed. In this paper, four MBRs equipped with hollow-fibre polyvinylidene fluoride ultrafiltration membranes were operated continuously. The cleaning method applied consisted of sonication at low power (15 W) with different frequencies (20, 25, 30, and 40 kHz) for each module and aerated backwashing. The different MBRs were analysed comparatively between them and with a conventional MBR in order to check the effects of the irradiated waves on membrane integrity, effluent quality and process performance. Effluent turbidity and chemical oxygen demand, total and volatile suspended solid concentration and activated sludge viscosity were affected by biomass fragmentation or membrane cake removal, mainly at lower frequencies. The best transmembrane pressure control was achieved at the frequency of 20 kHz without a significant effect on membrane integrity. The results showed that under these operational conditions, no negative effects on effluent quality or membrane integrity were found, suggesting that this method was suitable for this type of membrane.