A stack to stack microbial fuel cell power to batteries storage was investigated on the pilot scale with the aim to scale up in future. A 12 unit MFC-stack, equipped with maximum power point tracking (MPPT) and lithium polymer batteries (3.7 V), was set up. The MFC-stack architecture was simplified by sharing partially electrolytes. The serial 12 unit MFC-stack was first used as a linear assembly of all MFC units and then subdivided into three MFC-sub-stacks which enhanced power extraction by 8.5 times. To balance the stack power generation, the external circuits were alternated into zigzag, braid and random figurations as well in rational directed configurations. Finally, batteries permutation along with MPPT enabled faster and balanced lithium battery stack charging. Balanced conditions resulted in time shift oscillations, the absence of unwanted power pooling and voltage reversals. All in all, the work showed how to generate and store power from an 12 L microbial fuel cell stack with partly common electrolytes.