Controlling nanoparticle organization in polymer matrices has been and is still a long-standing issue and directly impacts the performance of the materials. In the majority of instances, simply mixing nanoparticles and polymers leads to macroscale aggregation, resulting in deleterious effects. An alternative method to physically blending independent components such as nanoparticle and polymers is to conduct polymerizations in one-phase monomer/nanoparticle mixtures. Here, we report on the mechanism of nanoparticle aggregation in hybrid materials in which gold nanoparticles are initially homogeneously dispersed in a monomer mixture and then undergo a two-step aggregation process during polymerization and material processing. Specifically, oleylamine-functionalized gold nanoparticles (AuNP) are first synthesized in a methyl methacrylate (MMA) solution and then subsequently polymerized by using a free radical polymerization initiated with azobis(isobutyronitrile) (AIBN) to create hybrid AuNP and poly(methyl methacrylate) (PMMA) materials. The resulting products are easily pressed to obtain bulk films with nanoparticle organization defined as either well-dispersed or aggregated. Polymerizations are performed at various temperatures (T) and MMA volume fractions (ΦMMA) to systematically influence the final nanoparticle dispersion state. During the polymerization of MMA and subsequent material processing, the initially homogeneous AuNP/MMA mixture undergoes macrophase separation between PMMA and oleylamine during the polymerization, yet the AuNP are dispersed in the oleylamine phase. The nanoparticles then aggregate within the oleylamine phase when the materials are processed via vacuum drying and pressing. Nanoparticle organization is tracked throughout the polymerization and processing steps by using a combination of transmission electron microscopy (TEM) and small-angle X-ray scattering (SAXS). The resulting dispersion state of AuNPs in PMMA bulk films is ultimately dictated by the thermodynamics of mixing between the PMMA and oleylamine phases, but the mechanism of nanoparticle aggregation occurs in two steps that correspond to the polymerization and processing of the materials. Flory–Huggins mixing theory is used to support the PMMA and oleylamine phase separation. The reported results highlight how the integration of nonequilibrium processing and mean-field approximations reveal nanoparticle aggregation in hybrid materials synthesized by using reaction-induced phase transitions.