Anaerobic treatment processes have achieved popularity in treating palm oil mill effluent due to its high treatability and biogas generation. The use of externally submerged membranes with anaerobic reactors promotes the retention of the biomass in the reactor. This study was conducted in thermophilic conditions with the Polytetrafluoroethylene hollow fiber (PTFE-HF) membrane which was operated at 55 °C. The reactor was operated at Organic Loading Rates (OLR) of 2, 3, 4, 6, 8, and 10 kg Chemical Oxygen Demand (COD)/m3·d to investigate the treatment performance and the membrane operation. The efficiency of the COD removal achieved by the system was between 93–98%. The highest methane yield achieved was 0.56 m3 CH4/kg CODr. The reactor mixed liquor volatile suspended solids (MLVSS) was maintained between 11.1 g/L to 20.9 g/L. A dead-end mode PTFE hollow fiber microfiltration was operated with the constant flux of 3 LMH (L/m2·h) in permeate recirculation mode to separate the clear final effluent and retain the biomass in the reactor. Membrane fouling was one of the limiting factors in the membrane bioreactor application. In this study, organic fouling was observed to be 93% of the total membrane fouling.