The filtration performance of flocculated and granulated configured anaerobic membrane bioreactors (MBR) treating domestic wastewater has been evaluated and compared to conventional aerobic MBR. Immersed hollow fibre (HF) and external tubular membrane geometries were additionally compared with the latter operated in both pumped and gas-lift mode. After 200 d of operation, both granular and flocculated anaerobic MBR (AnMBR) suspensions were characterised by an increased population of colloidal particles while the aerobic MBR retained a unimodal particle size distribution with a d50 of 20 μm. Consequently, the flocculated AnMBR supernatant was characterised by a soluble microbial product (SMP) concentration ca. 500% higher than the aerobic MBR, such that the lowest critical fluxes for both HF and tubular membranes were recorded for the AnMBR. In comparison, the granulated AnMBR sludge was characterised by a low mixed liquor suspended solids concentration and an SMP concentration below 50% that of the flocculated anaerobic MBR. Consequently, similar fluxes to those of the aerobic MBR were achieved with the granulated anaerobic sludge using immersed HF membranes. Operating external tubular membranes in gas-lift appeared less effective for the granular AnMBR than the Aerobic MBR. However, critical fluxes >40 L m−2 h−1 were achieved using pumped mode. Results suggest granular AnMBR systems to be most suited to domestic wastewater treatment using either immersed HF membranes or external tubular membranes in pumped crossflow mode.Highlights► Fouling within anaerobic membrane bioreactors treating temperate domestic wastewater is compared to aerobic MBR. ► Fouling potential of completely mixed flocculated reactors and granular upflow anaerobic reactors are directly compared. ► Immersed and external membrane geometries are compared for both anaerobic MBR reactors and the aerobic MBR.