Microbial Fuel Cells (MFCs) have been receiving increased interest in the last three decades. MFC can produce electrical energy from a wide variety of organic wastes in wastewater treatment plant concurrently with the treatment process. MFCs are considered as low power, low voltage generator. Scaled-up systems are needed to allow for efficient treatment of large volume of wastewater, but also to be able to produce sufficient electricity. Non-uniformities and hydraulic couplings between stacked MFCs are two problems that can negatively affect the performances. A power management unit is required to step-up the output voltage of the association of few MFCs for suitable supply of low power applications. In this paper, the operation of a serial stack, hydraulically coupled, non-uniform MFCs is studied and optimized to supply low power applications in a wastewater treatment scheme.