The scaling of microbial fuel cells (MFCs) for practical wastewater treatment and energy recovery depends on the development of high-performance, affordable, and sustainable separators. In this study, a polyvinyl alcohol (PVA) membrane separator devoid of per- and poly-fluoroalkyl substances (PFAS) was created and used in a biomimetic micro MFC for the treatment of municipal wastewater. By improving fluid dynamics and imitating natural vascular systems, the biomimetic channel design improved substrate–biofilm interaction. The manufactured PVA membrane operated in ambient settings without the requirement for external aeration, achieving a coulombic efficiency of 85.5% and a chemical oxygen demand (COD) elimination efficiency of 68±0.10%. Based on the anticipated material cost of 46.10 USD/ft2, it is eight times more cost-effective for practical applications than commercial Nafion membranes. Higher current density and consistent power production over extended operation were made possible by enhanced proton conductivity and decreased internal resistance, as demonstrated by electrochemical characterisation. Resilience over extended continuous-flow operation was demonstrated by the membrane's strong mechanical stability and anti-fouling capabilities. The suggested PFAS-free PVA membrane produced eight times more energy recovery per unit cost than traditional MFC separators, making it a practical option for decentralised wastewater treatment and sustainable energy production. The system's potential for use in off-grid energy recovery systems, rural sanitation facilities, and municipal wastewater treatment plants is highlighted by its low-cost scalability, bioinspired reactor architecture, and green chemistry in membrane production. In order to achieve the circular economy and the Sustainable Development Goals (SDGs) of clean water and affordable clean energy, this work shows how PFAS-free, biodegradable PVA membranes can be used to bridge the gap between laboratory research and industrial-scale MFC deployment.