Two laboratory-scale anaerobic membrane bioreactor (AnMBRs) were built to investigate the effect of zinc oxide nanoparticles (ZnO-NPs) on their performance, and the recovery phase was also examined. Results showed that the addition of ZnO-NPs with 0.4 mg/L caused significant deteriorations of AnMBR performance, including decrements of chemical oxygen demand (COD) removal efficiency from 96.4% to 81.5% and biogas production from 0.36 to 0 L/g COD removal within 40 days. A significant increment from 13.2 to 52.1 mg/L in soluble microbial products (SMP) was obtained, while no obvious effect on colloids was observed except an increased fluctuation of colloid concentration. Additionally, gas chromatography-mass spectrometry (GC-MS) analysis revealed remarkable changes of compounds in effluent with exposure to ZnO-NPs, and some new alkanes and esters were produced, such as Cyclobutane, 1,2-diethyl-, trans-, Tetradecane, Cyclopropane, octyl-, and Butanoic acid, methyl ester. The microbial community was compared using high-throughput sequencing, clearly showing the changes in both bacteria and archaea communities. Furthermore, results for recovery phase indicated that the AnMBR performance can be recovered within around 60 days after stopping ZnO-NPs addition, accompanied by the decrement of zinc concentration mainly adsorbed by sludge.