In the present study a pilot-scale ceramic membrane bioreactor (MBR) system was used for the treatment of simulated municipal wastewater. With the introduction of excess phosphorus to the bioreactor, a gradual deterioration of the membrane filtration performance and eventual failure of the pilot system was observed. A detailed investigation performed on the mixed liquor showed that phosphorus related calcium and magnesium complexes accumulated in the bioreactor. Under excess phosphorus conditions, these crystals caused abrasion of the membrane active filtration layer, leading to higher permeability, extensive membrane fouling, and eventual replacement of the membrane unit. A thorough comparison was conducted between the deteriorated membrane and a new module, using X-ray Diffraction (XRD), mercury and gas adsorption porosimetry, scanning electron microscopy (SEM), and electron dispersive X-ray (EDX). Porosimetry tests clearly demonstrated that the effective pore size of the deteriorated membrane shifted to higher values. SEM and EDX analysis showed that the active filtration layer composed of zirconia was sheared off entirely. Trace amounts of calcium were detected on the top layer, verifying calcium related abrasion of the filtration surface.