Microfiltration can clarify pomegranate juice; however, fouling is a limiting phenomenon in the process. In current work ultrasound was applied above and below the membrane surface to reduce fouling after removing temperature effect. A hydrophilic mixed cellulose ester membrane with pore size of 0.45 μm was used in lab scale flat sheet module. Membrane module was placed above and below the ultrasonic probe with frequency of 30 kHz and power of 1000 W, separately. The feed temperature in ultrasonic-membrane process was recorded and the experiment was repeated without ultrasonic treatment in similar feed temperature. Results showed that ultrasonic treatment above the membrane surface can increase the permeate flux; however, difference between the permeate fluxes was only before the steady state condition. On the other hand, the ultrasonic treatment below the membrane surface compared with the process which was performed without ultrasonic treatment cannot change the permeate. Also standard blocking was the main fouling mechanism in the membrane process which was equipped with the ultrasound probe above and below the membrane surface. Evaluation of blocking index showed that the cake formation is the main fouling mechanism all over the time in the process where ultrasound probe was inserted above the membrane surface. However, inserting the ultrasound probe below the membrane surface changed the value of blocking index. In this configuration cake formation was followed by intermediate blocking, standard blocking and complete blocking.