Epoxy adhesive systems were formulated and tested for their bonding behavior. Fumed silica and elastomer type and concentration were varied for the purpose of investigating their influences on intermediate and final adhesive performance properties. Of special interest was analyzing the role that flexibilized elastomer, that which does not phase separate during cure, played in these properties. Adhesive systems were tested with a commercial prepreg system using both bonded and cocured geometries. Dynamic mechanical analysis and optical microscopy showed the phase separation of the rubber was significantly influenced by the silica addition. Elastomer-rich dispersed phase growth rates were depressed resulting in a lower percentage of toughening domains. Mode I and II fracture energies were a strong function of dispersed phase particle size, flexibilized elastomer type/content, and residual stress considerations at the resin-resin interface. There were distinct differences between bonded and cocured fracture results with bonded samples generally outperforming cocured specimens due to changes in the surface roughness, resin flow properties, and interfacial stress build-up. Collectively, this work illustrates the importance of phase separation behavior on the final part morphology and performance for liquid elastomer toughened epoxy adhesives.