The three-dimensional microstructure of ionic aggregates in Zn-neutralized sulfonated polystyrene ionomers was characterized, for the first time, by transmission electron tomography. Two methods were used in order to prepare ionomer films: the hot-pressing and solvent-casting. With the first method, spherical aggregates with a mean diameter of about 5 nm are observed within the material. They are heterogeneously dispersed within the matrix and tend to form a network. When the second processing method is used, a nanoplatelet shape (with a thickness of about 6 nm) is unambiguously observed for the ionic aggregates. A preferential alignment of these aggregates parallel to the film plane is induced by this method. The solvent-casting process is a very slow method where the medium viscosity is gradually increasing; such an aggregate morphology is assumed to represent a complete aggregation state for the ionic groups.