Abstract Membrane integrity was evaluated for a pilot scale anaerobic fluidized bed membrane bioreactor (AFMBR) after operation for 765 days. Permeability and bubble point tests results for membrane specimens taken from the top of the membrane modules were similar to those of virgin membranes, thus no significant membrane damage was found at the top. On the other hand, membrane specimens taken from the middle and bottom sections were damaged severely by the continuous contact with fluidized 0.8–4 mm granular activated carbon particles as evidenced through scanning electron microscopy, as well as by permeability and bubble point tests. The occurrence of such significant membrane damage after only 2 years of operation indicates that membranes with a higher resistance to abrasion are desirable for use in the AFMBR.