Dissimilatory nitrate reduction to ammonium (DNRA) received more attention for its ability to recover ammonium. This study investigated the possibility of low-frequency infrared electromagnetic field (IR-EMF) to improve DNRA. The optimal IR-EMF intensity of 0.04 μT could effectively improve DNRA activity of nonwoven fabric membrane bioreactors. In the long-term operation, the average ammonium conversion efficiency was enhanced by 117.7% and 62.5% under 0.04 μT and 0.06 μT IR-EMF, respectively. The highest nrfA-gene abundance and potential DNRA rate were obtained under 0.04 μT IR-EMF exposure. Bacteroidetes fragilis, Shewanelle oneidensis MR-1, and Thauera sp. RT1901 were selected to investigate the dynamic response of nitrogen transformation and energy metabolism to IR-EMF. The transcriptome sequencing and RT-qPCR results suggested that IR-EMF could enhance both denitrification and DNRA process, mainly by improving ATP synthesis to boost metabolic activity. This study provided an efficient method for the nitrogen recovery via DNRA process by applying IR-EMF.