Proton exchange membrane water electrolysis (PEMWE) is needed to store renewable energy in the form of hydrogen. To improve the performance of PEMWE, elucidating the degradation mechanism of iridium (Ir)-based catalysts used for oxygen evolution reaction (OER) that is a rate-determining step is important. To date, it is known that one important reason for that is undesirable change in crystal structure of Ir. To further evaluate its degradation mechanism, in this study, effects of operating voltage conditions on crystal structure of Ir are investigated because the voltage conditions can accelerate changes in crystal structure of Ir. Especially how Ir was changed into an unfavorable metallic form was analyzed. PEMWE single cells under conditions of (i) a constant voltage of 1.9 V, (ii) a voltage cycle of 1.7–1.9 V, then a constant voltage of 1.9 V, and (iii) an applied voltage cycle with open circuit voltage (OCV). In the OCV condition, the crystalline structure of Ir was irreversibly transformed into a metallic form. This transformation induced lower OER activity than other crystalline states of Ir, followed by lower performance of PEMWE single cells. These findings help to establish baseline protocols for the stable operation of PEMWEs using Ir-based catalysts.