Developing a hybrid composite polymer membrane with desired functional and intrinsic properties has gained significant consideration in the fabrication of proton exchange membranes for microbial fuel cell applications. Among the different polymers, a naturally derived cellulose biopolymer has excellent benefits over synthetic polymers derived from petrochemical byproducts. However, the inferior physicochemical, thermal, and mechanical properties of biopolymers limit their benefits. In this study, we developed a new hybrid polymer composite of a semi-synthetic cellulose acetate (CA) polymer derivate incorporated with inorganic silica (SiO2) nanoparticles, with or without a sulfonation (–SO3H) functional group (sSiO2). The excellent composite membrane formation was further improved by adding a plasticizer (glycerol (G)) and optimized by varying the SiO2concentration in the polymer membrane matrix. The composite membrane’s effectively improved physicochemical properties (water uptake, swelling ratio, proton conductivity, and ion exchange capacity) were identified because of the intramolecular bonding between the cellulose acetate, SiO2, and plasticizer. The proton (H+) transfer properties were exhibited in the composite membrane by incorporating sSiO2. The composite CAG–2% sSiO2membrane exhibited a higher proton conductivity (6.4 mS/cm) than the pristine CA membrane. The homogeneous incorporation of SiO2inorganic additives in the polymer matrix provided excellent mechanical properties. Due to the enhancement of the physicochemical, thermal, and mechanical properties, CAG–sSiO2can effectively be considered an eco-friendly, low-cost, and efficient proton exchange membrane for enhancing MFC performance.