Ionomer nanocomposites provide a promising solution to address ion crossover issues inherent to traditional ion-containing membranes used in batteries for grid-scale energy storage (e.g., vanadium redox flow batteries). Herein, we investigate the impact of nanoparticle surface chemistry on nanoparticle dispersion, membrane morphology, and vanadium ion permeability in a series of Nafion nanocomposites. Specifically, silica nanoparticles (SiNPs) were functionalized with various chemical moieties, seven in total, that electrostatically interact, either attractively or repulsively, with the sulfonic acid groups that coalesce to form the ionic network within Nafion. As seen from electron microscopy analysis of the nanocomposites, SiNPs with sulfonic acid end-functionality were, on average, well dispersed within the ionomer membrane, though increased vanadium ion permeability, as compared to pristine (or unmodified) Nafion, was observed and attributed to changes in the Donnan potential of the system. In contrast, SiNPs with amine end-functionality were, on average, observed to form large aggregates within the ionomer membrane. Surprisingly, nanocomposites containing a higher degree of nanoparticle aggregation demonstrated the lowest vanadium ion permeability. Fractal analysis of the low-Q small-angle neutron scattering data suggests that the interface between the ionomer and the SiNP surface transitions from rough to smooth when the nanoparticle surface is changed from sulfonic acid-functionalized to amine-functionalized.