Due to the widespread presence of antibiotic resistance genes (ARGs) in traditional biological wastewater treatment systems, electrochemical disinfection techniques have received extensive attention. The rTNA/Sb-SnO2/PbO2 Reactive Electrochemical Ceramic Membrane (RECM) system has demonstrated outstanding performance in effectively removing refractory antibiotics. However, its capacity to remove antibiotic resistant bacteria (ARB) remains unclear. In this study, an antibiotic resistant strain of Escherichia coli (AR E. coli) was employed to investigate the disinfection efficiency of the RECM system at a macroscopic level, along with its disinfection mechanism at a microscopic level. Furthermore, the secondary effluent from an antibiotic production wastewater treatment plant was collected to validate the disinfection performance of this system against ARB in actual wastewater. In the RECM system, the inactivation of AR E. coli and the removal of ARGs were primarily governed by the electrocatalytic process, with notable influences from critical factors such as current density, electrolyte type, and hydraulic retention time. Morphological observation and flow cytometry experiments confirmed that the AR E. coli in the RECM system was inactivated by alterations in cell morphology, leading to fragmentation, and by improvement in cell membrane permeability. More significantly, this system exhibited noteworthy efficiency in treating wastewater contaminated with antibiotic resistant pollutants, effectively eliminating both antibiotics and ARGs from the secondary effluent. Overall, our study comprehensively investigated the performance and underlying mechanisms of the RECM system in mitigating the dissemination of ARGs, as well as its potential feasibility of practical application.