Biocathodes in bioelectrochemical systems (BESs) have been reported to enhance nitrogen (N) removal. However, the complex multi-parameter variables in BESs have increased the difficulty of studying the enhanced mechanism of nitrification using biocathodes. This study aimed to construct a range of potentiostatic biocathodes (−400, −200, +200, and +400 mV vs Ag/AgCl) with a dissolved O2 concentration of 2–3 mg L−1 using a potentiostat to further clarify the mechanism. The mechanism of how biocathodes influence microorganisms was elucidated from multiple perspectives, including variations in N concentration, electrochemistry, high-throughput sequencing, and PICRUSt2 prediction. The biocathodes were found to increase the nitrification rate by improving the abundance of nitrification-related bacteria (unidentified_Nitrospiraceae, Thauera, Nitrosomonas, Prosthecobacter, and Stenotrophomonas), the expression of genes related to ammonia oxidation and nitrite oxidation (pmoABC, hao, nirk, ncd2, and npd), and the activity of ammonia oxidase (AMO) and nitrite oxidase (NOR) in the biocathodes. The results of this study might provide crucial academic support and demonstration in facilitating the application of BESs and realizing the deep treatment of wastewater.