Proton exchange membrane fuel cells (PEMFCs) represent one of the most interesting technologies for powering vehicles and small portable electronic devices in an eco-friendly way. Large scale implementation of PEMFCs requires to tailor novel resilient economically viable materials with prolongated lifetimes. One key issue is the durability of the ionomer membrane, which is responsible for the conduction of protons from anode to cathode. Here we report on the impact of aging on the membrane structure by means of operando SAXS. By analyzing the most prominent features of the in-situ aged and pristine spectra at different relevant positions in the fuel cell, we could establish that structural aging is highly heterogeneous and strongly dependent on the local conditions. The increase in current density produces a decrease in ionic nanodomain sizes in aged ionomer due to continuous membrane drying, as in pristine materials. However, long-term operation most dramatically affects the polymer organization into bundles, in particular at the air inlet and in the middle of the cell. Variations of the low-angle intensity of more than an order of magnitude are ascribed to significant increase in the area of interfacial regions, potentially impacting the diffusion within grain boundaries. With this study, we demonstrate that operando SAXS provides unique insights into ionomer structural aging in dependence of the local hydration and helps to identify the relevant scale for physical degradation. This information is needed for optimizing fuel cells operating strategies and improving the durability of membranes.