Cationic polymers have proven to be suitable flux enhancers (FEs) in large‐scale aerobic membrane bioreactors (MBRs), whereas in anaerobic membrane bioreactors (AnMBRs) research is scarce, and so far, only done at lab‐scale. Results from MBRs cannot be directly translated to AnMBRs because the extent and nature of membrane fouling under anaerobic and aerobic conditions are different. Our research focused on the long‐term effect of dosing the cationic polymer Adifloc KD451 to a pilot AnMBR, fed with source‐separated domestic blackwater. A single dosage of Adifloc KD451 at 50 mg L⁻¹ significantly enhanced the filtration performance in the AnMBR, revealed by a decrease in both fouling rate and total filtration resistance. Nevertheless, FE addition had an immediate negative effect on the specific methanogenic activity (SMA), but this was a reversible process that had no adverse effect on permeate quality or chemical oxygen demand (COD) removal in the AnMBR. Moreover, the FE had a long‐term positive effect on AnMBR filtration performance and sludge filterability. These findings indicate that dosing Adifloc KD451 is a suitable strategy for fouling mitigation in AnMBRs because it led to a long‐term improvement in filtration performance, while having no significant adverse effects on permeate quality or COD removal.