Thin and ultrathin polymer films combined with nanoparticles (NPs) are of significant interest as they are used in a host of industrial applications. In this paper we describe the stability of such films (hpoly ≤ 30 nm) to dewetting, specifically, how the development of a spinodal instability in a composite NP-polymer layer is controlled by the embedding of Au NPs. At working temperatures (T = 170 °C) above the polymer glass transition temperature (Tg ≈ 100 °C) the absence of Au NPs leads to film rupture by nucleation dewetting, while their presence over a large surface area enhances the development of a spinodal instability without destroying the film continuity. When the NPs embed, the surface undulations are suppressed. The dynamics change from an unstable to a stable state, and the thin composite NP-polymer layer returns to a flat configuration, while the wavelength of the pattern remains constant. Moreover, we demonstrate from a thermodynamic perspective that NPs will remain on the surface or embed in the polymer film depending on their free energy, which is determined by the NP interactions with the underlying polymer, the native SiOx layer, and the Si substrate.