Methanol-based electrolysis can be a prospective alternative for the reduction of energy consumption. Developing highly durable methanol-based electrolysers with small CO2 release can help achieve cheaper hydrogen. Further, to arrive at a circular economy in H2, recycling the precious components would play a major role. Several studies on catalyst recycling have overshadowed the need for recycling the proton exchange membrane. Membrane, which forms 25% of the device cost, need to be studied for its degradation and optimizing the operating parameters of the device have a big role to play in establishing recycling. Our previous studies concluded that the change in crystallinity of membrane from fuel cell was closely related to membrane properties. Herein, for the first time, we have correlated the crystallinity of the membrane retrieved from an electrochemical methanol-reformer to its degradation mechanism. The average crystallinity on the anode and cathode sides was observed to be increased drastically compared to a fuel cell. As observed from Fourier Transform Infrared Spectroscopy (FTIR), the presence of sulfonic acid anhydrides was considered one of the reasons for this increase in crystallinity. X-ray photoelectron spectroscopy (XPS) showed that carbon peaks in the side chain was devoid of α-OCF2, –CF3, indicating severe degradation. The probability of finding a degraded area on the anode side of the scanned recycled membrane was 88% and 55% for the cathode side. The severe degradation of amorphous side chains and formation of short chains had considerably increased the crystallinity. The disparity in the intensity of degradation on the anode and cathode sides of the membrane was confirmed by the percentage of crystallinity and XPS studies. Further, the severity of degradation on either side of the membrane from methanol-based Proton Exchange Membrane electrolysers makes them difficult for further reuse in hydrogen-based energy systems.