Microbial Fuel Cells (MFCs) offer the dual benefit of wastewater treatment and electricity generation, but their performance is often limited by electrode properties. This study evaluates the use of large-sized Zn-Cu electrodes in an MFC integrated with a Modified Septic Tank (MST-MFC), focusing on organic and nutrient removal, as well as energy output. The system consists of anoxic, anaerobic, aerobic, and sedimentation compartments, with the anode placed in the anaerobic zone and the cathode in the aerobic zone. Two recirculation ratios (RR), 20 and 30%, were tested to evaluate their effect on COD and ammonia removal efficiencies, and it showed that the 30% RR provided more stable and higher COD removal efficiencies, ranging from 62.27% to 93.85%, whereas the 20% RR achieved only 29.38–71.06%, in line with previous studies emphasizing the positive effect of recirculation on mass transfer. However, ammonia removal remained relatively low in both variations and did not comply with the regulatory discharge standards. In terms of energy production, the MFC equipped with Zn-Cu electrodes generated power densities of 251.1 mW/m2 for the 30% RR and 129.58 mW/m2 for the 20% RR—significantly higher than those reported in studies using bioelectrodes such as carbon and graphite. These findings suggest that while MFCs hold promise for effective organic pollutant removal, further optimization is required to enhance nutrient—particularly ammonia—removal in high-strength wastewater. Additionally, long-term considerations for electrode material selection are crucial to ensure not only high electricity output but also effective treatment performance.