Chitosan (CS), a promising potential biopolymer with exquisite biocompatibility, economic viability, hydrophilicity, and chemical modifications, has drawn interest as an alternative material for proton exchange membrane (PEM) fabrication. However, CS in its original form exhibited low proton conductivity and mechanical stability, restricting its usage in PEM development. In this work, chitosan was functionalized (sulfonic acid (-SO3H) groups)) to enhance proton conductivity. The sulfonated chitosan (sCS) was blended with polyvinylidene fluoride (PVDF) polymer, along with the incorporation of functionalized SiO2 (–OH groups), for fabricating chitosan-based composite proton exchange membranes to enhance microbial fuel cell (MFC) performances. The results show that adding functionalized inorganic fillers (fSiO2) into the membrane enhances the mechanical, thermal, and anti-biofouling behavior. From the results, the PVDF/sCS/fSiO2 composite membrane exhibited enhanced proton conductivity 1.0644 × 10−2 S cm−1 at room temperature and increased IEC and mechanical and chemical stability. Furthermore, this study presents a revolutionary way to generate environmentally friendly natural polymer-based membrane materials for developing PEM candidates for enhanced MFC performances in generating bioelectricity and wastewater treatment.