Heavy metal removal and simultaneous energy production were studied using a dual chambered Microbial Fuel Cell inoculated with Shewanella oneidensis MR‐1 in the anode. Synthetic wastewater was prepared with Cu (II), Mg (II), Mn (II), Zn (II), Na, and Phenol based on desalter effluent from refinery processes at different metal concentrations. In this study, a maximum open‐circuit voltage of 517.6 mV was reached at Conc. 5 with wastewater in the anode chamber, and 127.7 mV at Conc. 3 was produced with synthetic wastewater in the cathode chamber. Moreover, μ at Conc. 5 was 0.1133 h−1, demonstrating bacterial growth under metal and phenol concentrations. The highest metal removal in the anode for Cu (II), Mg (II), Mn (II), Zn (II), and Na was 93%, 85%, 93%, 88%, and 36%, respectively. In the cathode chamber the removal of Cu (II), Mg (II), Mn (II), Zn (II), and Na was 98%, 49%, 57%, 59%, and 36%, respectively. During the operation in the anode, SEM images showed that the bacterial nanowires are formed in response to toxic and anaerobic environments which contribute to the bacterial growth. These nanowires increased the metal removal and the voltage production as a consequence of a higher electron rate from the anode to the cathode due to the higher extracellular membrane surface area. S. oneidensis is a bacterium with metal‐reducing characteristics, and it is suitable for metal removal and electron transport from carbon sources, demonstrated in voltage production with microbial fuel cells.