The introduction of nanoparticles into the polymer matrix is a useful technique for creating highly functional composite membranes. Our research focuses on the development of nanoparticle-filled proton exchange membranes (PEMs). PEMs play a crucial role in efficiently controlling the electrical energy conversion process by facilitating the movement of specific ions. This is achieved by creating functionalized nanoparticles with polymer coatings on their surfaces, which are then combined with resins to create proton-conducting membranes. In this study, we prepared PEMs by coating the surfaces of silica nanoparticles with acidic polymers and integrating them into a basic matrix. This process resulted in the formation of a direct bond between the nanoparticles and the matrix, leading to composite membranes with a high dispersion and densely packed nanoparticles. This fabrication technique significantly improved mechanical strength and retention stability, resulting in high-performance membranes. Moreover, the proton conductivity of these membranes showed a remarkable enhancement of more than two orders of magnitude compared to the pristine basic matrix, reaching 4.2 × 10−4 S/cm at 80 °C and 95% relative humidity.