Polymer membranes used in the proton exchange membrane fuel cell (PEMFC) technology are subject to severe chemical and physical degradations during operation. A microscopic diagnosis of the effects of aging on the microstructure of benchmark perfluorinated sulfonic acid (PFSA) membranes is crucial to developing long-lasting devices. We report here the first μSAXS study of membranes aged for 2500 h in a stack. SAXS spectra recorded with submicrometer resolution in-plane and along the membrane thickness provide a 3D mapping of the aging effect. Nanoscale heterogeneities are evidenced and found to depend on the membrane position relative to the electrodes, to the air inlets, and proximity to channels (distributing gas) or ribs (collecting the current). Long-term aging in a fuel cell operating in stationary conditions around 65 °C results in a small voltage degradation rate of 13 μV/h, without any evidence of membrane failure, but to an irreversible over-swelling of the membrane due to polymer relaxation. Regions under the gas distribution channels close to the air inlet are profoundly degraded due to an increased water gradient concentration from the cathode to the anode. These observations provide a novel and unique insight for developing new strategies toward the design of more durable polymers inserted in smart fuel cells.