One limiting aspect to make microbial fuel cells (MFCs) a viable technology is to obtain low cost and environmentally sound materials for their components. In this work we synthesized membranes by a simple procedure involving low price and biodegradable materials such as poly (vinyl alcohol) (PVA), chitosan (CS) and PVA:CS, all cross-linked with sulfuric acid; they were compared to Nafion®, as our reference/control membrane. PVA:CS show lower oxygen permeability in comparison to Nafion® membranes, a strong advantage in order to maintain anaerobic conditions in the anodic compartment of MFCs. Membranes were characterized in typical H-Type MFCs, and results show that PVA:CS membranes outperform Nafion® 4 times (power production) while being 75 times more economic. Moreover, we design a paper-based micro-scale MFC, which was assayed as a toxicity biosensor; we obtained results in less than 20 min using 16 μL volume samples containing formaldehyde as a model toxicant. The PVA:CS membrane presented here can offer low environmental impact (materials, fabrication and disposal) and become a very interesting option for point of need single use disposable analytical devices.