To reduce membrane fouling during the processing of highly pulpy fruit juices into clarified beverages, a crossflow Sono-Microfiltration (SMF) system was employed, strategically equipped with an ultrasonic probe for the direct application of low-frequency ultrasound (LFUS) to the juice just before the entrance to the ceramic membrane. Operating conditions were standardized, and the application of LFUS pulses in both corrective and preventive modes was investigated. The effect of SMF on the physicochemical properties and the total soluble phenol (TSP) content of the clarified juice was also evaluated. The distance of ultrasonic energy irradiation guided the selection of the LFUS probe. Amplitude conditions and ultrasonic pulses were more effective in the preventive mode and did not cause membrane damage, reducing the operation time of jackfruit juice by up to 50% and increasing permeability by up to 81%. The SMF did not alter the physicochemical parameters of the clarified juice, and the measured LFUS energy ranges did not affect the TSP concentration during the process. This study is the first to apply LFUS directly to the feed stream in a pilot-scale crossflow microfiltration system to reduce the fouling of ceramic membranes and maintain bioactive compounds in jackfruit juice.