This work aims to encourage the use of natural materials for advanced energy applications, such as proton exchange membranes in fuel cells. Herein, a new conductive membrane produced from cassava liquid waste was used to overcome environmental pollution and the global crisis of energy. The membrane was phosphorylated through a microwave-assisted method with different phosphoric acid, (H3PO4) concentrations (10–60 mmol). Scanning electron microscopy (SEM), X-ray diffraction analysis (XRD), dynamic mechanical analysis (DMA), swelling behavior test, and contact angle measurement were carried out on the membrane doped with different H3PO4 levels. The phosphorylated NdC (nata de cassava) membrane doped with 20 mmol (NdC20) H3PO4 was successfully modified and significantly achieved proton conductivity (maximum conductivity up to 7.9 × 10−2 S cm−1 at 80 °C). In addition, the fabricated MEA was assembled using an NdC20 membrane with 60 wt% Pt/C loading of 0.5 mg cm−2 for the anode and cathode. Results revealed that a high power density of 25 mW cm−2 was obtained at 40 °C operating temperature for a single-cell performance test. Thus, this membrane has the potential to be used as a proton exchange membrane because it is environment-friendly and inexpensive for fuel cell applications.