To test the viability of incorporating a stacked-microbial fuel cell (SMFC) within a typical septic tank, 15 cartridges of MFCs with proton exchange membrane without catalysts were installed in a real system considered with a pretreatment. Both chemical oxygen demand (COD) removal and electricity generation using super capacitors by electricity storage were investigated under continuous flow mode. Three MFCs A1, B4 and C2 with 109.40 ± 34.25 mW/m3, 131.58 ± 27.75 mW/m3 and 124.01 ± 27.57 mW/m3, respectively, were chosen for testing. The organic loading rate was 0.24, 0.52 and 1.05 kg DQO/m3-d corresponding to 200, 500 and 1000 ppm. Total COD removal and total coulombic efficiency were 89.67 ± 5.19% and 48.07 ± 2.33%. The results of this study suggest that MFCs may be suitable for deployment in a septic tank. This research has demonstrated the great challenges in applying a stack of MFC in scale-up. Rint showed that anode resistances are higher than cathode; however, the configuration seems to be indicated for this kind of system depuration in developing countries. An electrochemical model must be developed for scale up which explains performance and electrochemical data. It is necessary to develop experiments in scale up and to test the feasibility of implementation.