The aim of this work is the optimization of electrospun polymeric nanofibers as an ideal reservoir of mixed electroactive consortia suitable to be used as anodes in Single Chamber Microbial Fuel Cells (SCMFCs). To reach this goal the microorganisms are directly embedded into properly designed nanofibers during the electrospinning process, obtaining so called nanofiber-based bio-composite (bio-NFs). This research approach allowed for the designing of an advanced nanostructured scaffold, able to block and store the living microorganisms inside the nanofibers and release them only after exposure to water-based solutions and electrolytes. To reach this goal, a water-based polymeric solution, containing 5 wt% of polyethylene oxide (PEO) and 10 wt% of environmental microorganisms, is used as the initial polymeric solution for the electrospinning process. PEO is selected as the water-soluble polymer to ensure the formation of nanofiber mats offering features of biocompatibility for bacteria proliferation, environment-friendliness and, high ionic conductivity. In the present work, bio-NFs, based on living microorganisms directly encapsulated into the PEO nanofiber mats, were analyzed and compared to PEO-NFs made of PEO only. Scanning electron microscopy allowed researchers to confirm the rise of a typical morphology for bio-NFs, evidencing the microorganisms’ distribution inside them, as confirmed by fluorescence optical microscopy. Moreover, the latter technique, combined with optical density measurements, allowed for demonstrating that after electrospinning, the processed microorganisms preserved their proliferation capability, and their metabolic activity after exposure to the water-based electrolyte. To demonstrate that the energy-production functionality of exo-electrogenic microorganisms was preserved after the electrospinning process, the novel designed nanomaterials, were directly deposited onto carbon paper (CP), and were applied as anode electrodes in Single Chamber Microbial Fuel Cells (SCMFCs). It was possible to appreciate that the maximum power density reached by bio-NFs, which resulted in being double of the ones achieved with PEO-NFs and bare CP. SCMFCs with bio-NFs applied as anodic electrodes reached a current density value, close to (250 ± 5.2) mA m−2, which resulted in being stable over time and was comparable with the one obtained with carbon-based electrode, thus confirming the good performance of the whole device.