Biofouling impedes the performance of anaerobic membrane bioreactors. In this study, we aim to determine if copper oxide (CuO) and zinc oxide (ZnO) nanoparticles can effectively delay the biofouling of polyethersulfone (PES) membranes without disseminating emerging contaminants like antibiotic resistance genes (ARGs) and metal resistance genes (MRGs). A consequential decrease in biofilm composition related to total cells, polysaccharides, proteins, and bioactivity (i.e., adenosine triphosphate (ATP) and quorum sensing (QS) signal molecules) was observed in the presence of heavy metal nanoparticles. Metagenomic and metatranscriptomic analyses further attributed the delay of biofilm formation to the lower expression of QS-associated genes and biofilm formation genes. It was also determined that the expression of ARGs and MRGs was not stimulated in the presence of CuO and ZnO nanoparticles. These findings collectively suggest that CuO and ZnO nanoparticles embedded in membranes can delay biofouling with minimal potential for disseminating ARGs and MRGs post-treatment.