Benthic microbial fuel cell (BMFC) is a futuristic technology for powering low power devices. A major problem in the scale‐up of BMFC is decreasing in the power generation with an increase in the size of the electrodes. However, the multi‐electrodes have a potential to increase the power generation. Therefore, multi‐electrodes (three electrodes) in Horizontal (H) and Vertical (V) configurations are examined in this work. For effective understanding, individual and combined electrodes in both the configurations are analyzed and compared with the Single (S) electrode. The analytical techniques, such as power and electrochemical impedance spectroscopy (EIS) are used in situ to understand the performance of BMFC. The start‐up provides information that the position of the electrode is the key for the enhancement of power generation. V, H, and S generated a maximum power density of 56.6, 49.4 and 22.5 mW m−2 having internal resistances of 389, 421 and 668 Ω, respectively. EIS data shows that the energy generation is dependent on the capacitance and resistance. The vertical arrangement provided the best configuration.