Electrochemical methanogenesis is a promising and reliable process to convert waste streams into CH4, where the electroactive methanogenic biofilms play a key role. However, given that microplastics (MP) have now been spread ubiquitously in the environment, their regulation on the performance and succession of methanogenesis biofilm remains an enigma. Herein, we developed the single-chamber electrochemical methanogenic systems to investigate how poly (ethylene terephthalate) MP (PET-MP) regulates methanogenic biofilm formation and microbial metabolisms. The microbial volume of biofilm formed under MP exposure was similar to that without exposure. However, the live/dead cell ratio of the microbes in the biofilm under the PET-MP exposure decreased significantly (p < 0.05). Correspondingly, the richness and diversity of the microbial community in the presence of MP were also lower. Network analysis implied the interspecific cooperation among the microbial communities to cope with the MP stress. Meanwhile, the biofilm produced more extracellular polymer substrates during the biofilm thickening, possibly as a defense against MP invasion. At the gene level, the content of methanogenic gene mcrA was found to positively linearly correlate with the cultivation cycles, both in presence (r = 0.945, p < 0.05) or absence of PET-MP (r = 0.913, p < 0.05). The outcomes of this study could provide insights into the practical application of electrochemical methanogenesis technology to upcycle the MP-polluted biowastes and to implement the Power&Waste-to-X concept better.