This study focuses on the use of fluidized resin beads to mitigate fouling during ultrafiltration (UF) of the effluent of an anaerobic bioreactor. Two different module configurations were tested: A fluidized bed of resin beads was generated in a tubular UF membrane, and a hollow fiber (HF) UF membrane was submerged into a fluidized bed, respectively. During filtration of anaerobically treated synthetic wastewater using the tubular module, fluidized resin beads with a diameter of 0.5–0.71 mm did not show any beneficial effect. In contrast, the presence of fluidized resin beads (diameter of 0.5–0.71 and 1.00–1.25 mm) in the HF module reduced the fouling rate significantly. Furthermore, particle diameter and the bed voidage affected the cleaning efficiency of a pre-fouled membrane in the HF module. Interestingly, short-term filtration tests (<2 h) of a dextran solution showed that fluidized resin beads are able to minimize concentration polarization of a macromolecule, even in the tubular module. Therefore, it is supposed that fouling of the anaerobically treated synthetic wastewater was mainly attributed to the deposition of colloidal and particulate matter.