Abstract Anaerobic membrane bioreactor (AnMBR) processes are a promising method of recovering energy from municipal wastewater. In this study, a pilot-scale AnMBR with extremely short hydraulic retention time (HRT = 2.2 h) was operated at a flux of 6 L/(m2h) for 340 days without any membrane cleaning. The average value achieved for chemical oxygen demand (COD) removal was 87% and for methane yield was 0.12 L CH4/gCODremoved. Based on mass balance analysis, it was found that about 30% of total influent COD was used for methane conversion, 15% of COD for sulfate reduction, 10% for biomass growth and 10–20% of COD remained in the effluent. Microbial community analyses indicated that seasonal changes of feedwater (in terms of organic components and temperature) led to the variations of microbial community structures. Among the bacterial communities, Chloroflexi, Proteobacteria and Bacteroidetes were the three most predominant phyla. In the archaeal consortia, WCHA1-57 and Methanobacterium surpassed Methanosaeta and Methanolinea to become the predominant methanogens during the long-term operation of short HRT. The sulfate-reducing bacteria, accounting for less than 2% of total abundance of bacteria, might not be the dominant competitor against methanogens.