In recent years, the quest to advance fuel cell technologies has intensified, driven by the imperative to reduce reliance on hydrocarbon-derived fuels and mitigate pollutant emissions. Proton exchange membranes are a critical material of fuel cell technologies. The potential of ionic liquid-based polymer inclusion membranes or ionogels for proton exchange membrane fuel cells (PEMFCs) has recently appeared. Thermal stability, SEM-EDX characterization, NMR and IR characterization, thermogravimetric analysis, ion exchange capacity, and water uptake are key properties of these membranes which need to be investigated. In this work, ionogel based on quaternary ammonium salts, such as [N8,8,8,1+][Cl−], [N8,8,8,1+][Br−], and [N8-10,8-10,8-10,1+][Cl−] in various compositions with poly(vinyl chloride) are extensively studied and characterized based on those key properties. The best properties were obtained when a quaternary ammonium cation was combined with a bromide anion. Finally, ionogels are tested in microbial fuel cells. Microbial fuel cells based on the ionogel reach a maximum of 147 mW/m2, which represents 55% of the reference membrane (Nafion 212). These results indicate that we still have the possibility of improvement through the appropriate selection of the cation and anion of the ionic liquid. Overall, the promise of ionogel membranes as a viable alternative in fuel cell applications has been demonstrated.