In this research, we are reporting the application of microorganisms modified by a conducting polymer polypyrrole (Ppy) - for the improvement of microbial biofuel cells. The synthesis of polypyrrole was assisted by metabolic and other biochemical processes that occur in microorganisms. Therefore, in this research the reported Ppy formation method can be recognized as environmentally friendly. During herein reported synthesis of Ppy, the cell walls and some other structures of Aspergillus niger and Rhizoctania sp selected for this research were modified by the formed Ppy, which facilitated the transfer of electrical charge generated by microorganisms towards an electrode. Two electrochemical methods: (i) amperometric measurements at constant potential and (ii) scanning electrochemical microscopy (SECM) were applied for the evaluation of charge transfer efficiency and for the determination of electrochemical activity of Ppy-modified and non-modified cells. Two mediators (1,10-phenanthroline-5,6-dione (PD) or 9,10-phenanthrenequinone (PQ) and potassium ferricyanide (K-3[Fe (CN)(6)])) based redox system was applied for the assessment of charge transfer from above mentioned living cells. The amperometric signals registered for electrodes based on Ppy modified cells were over six times higher in comparison to that of electrodes based on non-modified cells. This effect is assigned to advanced electrical conductivity of Ppy-modified cell wall and/or to better permeability of charge transfer mediators through the membrane and/or cell wall of Ppy-modified cells. Fungi of Aspergillus niger, which showed few times higher electrochemical activity in comparison to Rhizoctania sp., were investigated by SECM. Electrochemical differences between Ppy-modified and non-modified cells have been confirmed by SECM results. Therefore, this eco-friendly Ppy-formation technique seems effective in improving the performance of electrochemical devices such as microbial fuel cells and/or cell-based biosensors.