We control nanoparticle (NP) dispersion by leveraging the entropic and enthalpic effects associated with mixing silica NPs grafted with polyisoprene (PI) chains into matrices of varying degrees of chemical dissimilarity. Previous work in this area has primarily focused on entropic factors alone, and hence, this work represents a significant advance over the current state-of-the-art. We show using a combination of transmission electron microscopy/small-angle X-ray scattering that mixing grafted particles with PI matrices of identical microstructure yields dispersion states as found in the literature for such entropic systems. However, replacing the PI matrix chains with dissimilar matrices leads to an introduction of enthalpic interactions that, in some cases, can drastically change the resulting morphology. In particular, while slightly different PI microstructures for the grafted and free chains only yield moderated differences, using styrene–butadiene copolymers as a matrix leads to a completely different behavior. In the last case, phase separation becomes more likely with the increasing graft length, while the PI system (whose behavior is dominated by entropic factors) shows the opposite behavior. Tuning the relative importance of enthalpic versus entropic factors is thus another tool in controlling the self-assembled structure of NPs, which gives rise to enhanced macroscopic properties in the composite.