This study reports a large reinforcement of the plasmon–phonon coupling in alpha quartz achieved through the controlled deposition of gold nanoparticles into nano templates produced through chemical etching of ion tracks. Preferential agglomeration of nanoparticles within the etched ion tracks (nano wells) was observed in Scanning Electron Microscopy and Atomic Force Microscopy images. Raman characterization of quartz substrates with different nanoparticle concentrations revealed a relationship between the plasmon–phonon coupling intensity and nanoparticle concentration. Reinforcement of the plasmon–phonon coupling was observed as an increase in the Raman intensity with increasing concentration of deposited nanoparticles. The intensity initially increased linearly with nanoparticle concentration up to about 4 x 106 nps/µL where a saturation regime was identified. In the saturation regime, a roughly 200-fold increase in the scattering intensity was measured in the first micron of the specimen. At higher nanoparticle concentrations, the Raman intensity decreased exponentially following the Beer–Lambert Law. The reduction in the Raman intensity is attributed to increased laser absorption with increasing nanoparticle layer thickness. Comparatively weak reinforcement of Raman scattering was observed when nanoparticles were deposited on unirradiated and unetched samples, suggesting that the reinforcement of plasmon–phonon coupling may be favored by the anisotropic geometry of the nano wells. In particular, the etched tracks promote nanoparticles agglomeration likely promoting the formation of plasmon hotspots.