Proton exchange membrane water electrolysis (PEMWE) has gathered significant interest as a method for hydrogen production. A crucial step in optimizing PEMWE performance is a pre-treatment process known as “conditioning” or “break-in”, during which a voltage or current is applied to the PEMWE prior to its actual operation. Despite its importance, the underlying mechanisms and improvements achieved through conditioning remain unclear. This study investigates the effects of conditioning on PEMWE, focusing on changes in the properties of the cation exchange polymer electrolyte membrane and the IrO2 oxygen evolution catalyst. Results show that membrane conductivity increases and the valency of Ir changes from +3 to +5 by voltage application. The valency changes of Ir occur in two distinct voltage regions (0.8–1.0 and 1.3–1.5 V vs. cathode (CE)) when the applied voltage remains below the threshold for water electrolysis. Despite the intentional introduction of valence changes through applied voltage, no significant changes in the I-V characteristics within the water electrolysis region (from 1.5 to 2.0 V vs. CE) are observed. This is likely due to the fact that, at least as observed in linear sweep voltammetry, the activation time of Ir is sufficiently rapid that even the sweep rate of 10 mV/s is sufficient for activation.