This study probes the importance of preparation method, thermal treatment, and monomer structure in determining the nanoscale morphology of ionomers using both X-ray scattering and scanning transmission electron microscopy (STEM). A Cu-neutralized poly(styrene-ran-methacrylic acid) (SMAA) ionomer was isolated from solution by three different methods (room temperature solvent casting, solvent casting at elevated temperature, and precipitation) having different rates of nanoscale structure formation. While both solvent cast films exhibit typical ionomer scattering and uniform spherical ionic aggregates via STEM, the precipitated material shows no ionomer scattering peak and STEM imaging detects Cu-rich regions of various size, shape, and separation. Upon annealing the precipitated material, the morphology becomes indistinguishable from that prepared by solvent casting, indicating that thermal treatment drives the metastable morphology of precipitated Cu-SMAA ionomers toward a lower energy state. Next, the influence of chain packing on the self-assembly of nanoscale ionic aggregates was probed by comparing Cu-SMAA with Cu-neutralized poly(3-methylstyrene-ran-methacrylic acid) (3MeSMAA). When solvent cast, the ionic aggregates are larger in Cu-3MeSMAA than Cu-SMAA, though after annealing the two ionomers are indistinguishable by X-ray scattering and STEM. Thus, while solvent casting produces near-equilibrium morphologies in Cu-SMAA, this method produces a metastable morphology in Cu-3MeSMAA. In this ionomer, near-equilibrium ionic aggregates are promoted by ensuring both slow morphological development while isolating the neutralized polymer from solution and sufficient chain mobility to maximize the local ionic interactions between the anions and cations in the ionic aggregates. More broadly, the data from Cu-3Me-SMAA constitute the first report of direct correspondence between a change in the position of the ionomer scattering peak and an increase in ionic aggregate size as observed in STEM.