A material-sensitive atomic force microscopic (AFM) tapping mode was combined with current measurements to investigate structure, phase separation, and conductive structure of surfaces and cross sections of long side chain Nafion and short side chain AQUIVION PFSA ionomer membranes. We found unexpected large-scale ordered structures consistent with a dominant lamellar polymer structure at the cross sections. The highly terraced areas of both ionomers have a wide distribution of layer thicknesses from sub-nanometer to a few nanometers. In both broad size distributions, preferential sizes were identified that reflect the different lengths of the molecular side chains, indicating a stacking in layers. The nanoscale phase separation of the ionomer was analyzed by using the capacitive current distribution. In AQUIVION PFSA, larger connected water-rich ionic areas were found than in Nafion with same total ionic area. A steady-state current at the cross sections evolved only after an activation period by enforcing current flow though the membrane. A comprehensive and heterogeneous current distribution was observed with highly conductive areas. In contrast, on outer membrane surfaces, only non-continuous spot-like currents were observed. In general, our measurements are consistent with conduction in water layers in-between polymer chains and a bi-continuous structure under faradaic current flow. Perfluorinated sulfonated ionomer membranes (PFSA) have been established as proton-conducting electrolytes in many technical applications, most notably in brine electrolysis but also with increasing importance as electrolytes for fuel cell applications. For highperformance operation of fuel cells, the water management of the membrane is of great importance. Therefore, the nature of water transport and the conductive structure of the ionomer membrane are still under investigation. In particular, the nanoscopic ionomer properties at non-equilibrium conditions under steady-state current flow close to operation conditions are expected to differ from equilibrium state and have not been characterized in detail.During solidification of perfluorinated polymers (PFSA) casted from dispersions, a phase separation occurs that is the key factor in providing ionic conductivity. The hydrophilic sulfonate-terminated end groups of the side chains cluster together to form an ionic phase. The perfluorinated molecular backbone is assumed to form bundles due to the hydrophobic interaction and to undergo partial crystallization that is considered to enhance mechanical strength.1 The size of these crystalline areas, as determined from scattering data, is reported to be within 0.5 to 10 nm.2,3 The spacing of the average hydrophobic/hydrophilic separations was obtained from the position of the ionomer peaks in scattering data and determined to approximately 3-7 nm depending on the water content.4 While the hydrophobic phase provides mechanical stability, the ionic phase provides a waterbased proton-conducting network. It is generally assumed that this i...