In a groundbreaking study, Akcora group has shown that poly(ethylene oxide), PEO, nanocomposites with dynamically asymmetric, heterogeneous interfaces present a unique and reversible thermal-stiffening behavior above the glass transition temperature of the adsorbed polymer (Senses, E. et al., ACS Appl. Mater. Interfaces2015, 7, 14682–14689.). However, chemically heterogeneous interfaces can be fragile under severe shear fields that are common in continuous polymer processes. The current study is inspired by the work done in Akcora group on thermally-stiffening polymer nanocomposites and is aimed at understanding the effect of continuous processing operations such as extrusion on the structure and properties of thermally-stiffening nanocomposites. The effect of processing on nanocomposites of PEO and colloidal silica, SiO2, were investigated via thermogravimetric analysis (TGA), scanning electron microscopy (SEM), small and wide angle X-ray scattering, attenuated total reflectance-Fourier transform infrared (ATR-FTIR), and rheometry. Three types of silica nanoparticles were employed in the current study (while keeping the average silica nanoparticle size and concentration constant: 40–50 nm diameter and 30% by weight): bare silica, silica adsorbed with polycarbonate (PC), and silica adsorbed with poly(2–vinyl pyridine), P2VP. The adsorption of PC and P2VP onto silica creates a dynamically asymmetric, heterogeneous interface that is quite different compared to homogeneous interfaces where either nanoparticle surfaces are chemically modified with small chemical groups or with long grafted chains. The results indicated that upon extrusion, the average size of secondary agglomerates either remained unchanged or decreased slightly but the amount of agglomeration increased leading to deterioration of silica nanoparticle dispersion and viscoelastic properties (at temperatures below the glass transition temperature of the adsorbed polymer). Among the three systems studied, P2VP-adsorbed silica containing samples showed the largest degradation of viscoelastic properties upon extrusion, which was attributed to the desorption and disentanglement within the heterogeneous interface or to agglomeration leading to breaking of the percolated structure formed by nanoparticles and polymer bridges.