To modernize wastewater treatment plants, a pilot-scale anaerobic/anoxic/oxic-vibrating membrane bioreactor (A2/O-VMBR) was developed and successfully operated. Despite a low C/N ratio, the A2/O-VMBR achieved removal rates of 61.10%, 93.77%, 72.86%, and 54.75% for COD, TN, TP, and NH3-N, respectively. The maximum and extremity transmembrane pressures were 45 kPa, and 80 kPa, respectively, with no sludge bulking observed. The VMBR saved over 96–98% of energy compared to traditional MBR plants, making it a better option for municipal wastewater treatment. High-throughput sequencing analysis revealed identical bacterial population structures in samples obtained from the treatment units, with genera having nitrifying, denitrifying, hydrolyzing, and glycogen-accumulating activities, which allowed for nitrogen removal. The key functional microorganisms responsible for nitrification–denitrification were species belonging to the genera FCPU426, Fusobacteria, Planctomycetes, Verrucomicrobia, and Epsilonbacteraeota. The integrated experimental system produced favorable results in improving wastewater quality, highlighting the usability of the A2/O-VMBR technology. Therefore, this technique holds potential for further investigation into the context of wastewater treatment and recovery.