Microbial Fuel Cells (MFCs) harness the metabolism of micro-organisms to generate electrical energy from organic matter. MFCs offer great promise for simultaneous wastewater treatment and green energy production. The association of a large number of individual MFCs offers very interesting perspectives for electrical energy generation. It can scale-up the low output voltage of an individual cell to enable output voltages to levels acceptable by commercially-available DC/DC converters and it permits to mutualize the electrical powers of each cell. The serial association of a large number of MFCs is a challenge itself for many reasons. Firstly the hydraulic couplings (when MFCs share the same substrate) witch cause leakage of electrical-charge careers between the connected reactors. Secondly the non-uniformities between generators which lead to a non-optimal energy recovery because the associated cells do not able to operate at Maximum Power Point (MPP). Non-uniformities can be compensated with electronic circuits to prevent voltage reversal or enable voltage equalizing. In this paper a balancing method is studied and adapted for energy harvesting from a stack of serially connected MFCs. The balancing circuit was simulated, realized and tested for energy harvesting. With balancing method the cell voltage of MFCs in a stack can be equalized and the performance of MFCs can be improved and it leads to an optimal energy recovery of the stack.