In this study, polyethersulfone (PES) ultrafiltration membrane surface was modified with nano-sized zinc oxide (nZnO) and silver (nAg) to improve the membrane filterability of the mixed liquor and used to treat fruit-juice industry wastewater in a submerged membrane bioreactor (MBR). The nAg was synthesized using three different methods. In the first method, named as nAg-M1, PES membrane was placed on the membrane module and nAg solution was passed through the membrane for 24 h at 25 ± 1 °C. In the second method, named as nAg-M2, PES membrane was placed in a glass container and it was shaken for 24 h at 150 rpm at 25 ± 1 °C. In the third method, named as nAg-M3, Ag nanoparticles were loaded onto PES membrane in L-ascorbic acid solution (0.1 mol/L) at pH 2 for 24 h at 150 rpm at 25 ± 1 °C. For the preparation of nZnO coated membrane, nZnO nanoparticles solution was passed through the membrane for 24 h at 25 ± 1 °C. Anti-fouling performance of pristine and coated membranes was examined using the submerged MBR. The results showed that nZnO and nAg-M3 membranes showed lower flux decline compared with pristine membrane. Moreover, pristine and coated PES membranes were characterized using a permeation test, contact angle goniometer, and scanning electron microscopy.