In microbial electrolysis cells (MEC) proton exchange membranes (PEM) mainly Nafion 117 (N117) have many drawbacks regardless of their superior performance that lead to hinderance in scaling up efforts. Some of those drawbacks include the extremely high cost of N117 amount to about 40-60% of the total cost of the material, in addition, to biofouling concerns that limit proton transfer through the membrane, leading to performance deterioration. Other concerns include low selectivity towards protons and difficulty of membrane disposal. In this regard, a biocompatible, biodegradable and economically friendly PEM were prepared from chitosan (CS) biopolymer of 2wt% enforced with polyacrylonitrile (PAN) electrospun nanofiber mats. CS is a naturally abundant biopolymer with high hydrophilicity and non-toxicity; chemical and physical modification by crosslinking with sulfuric acid and impregnating it with PAN nanofiber respectively can enhance its mechanical stability and proved to increase it’s suitability for MEC application. The prepared membrane (PAN/CS) had a higher hydrophilicity and performance when applied in MEC at a much lower cost and ease of fabrication. For analysis and performance comparison PAN/CS has been tested against pristine N117 and CS membrane. The purpose of this study is to fabricate a suitable PEM for MEC performance at a considerably lower cost with equivalent performance and qualities.