Layers of thiophenol functionalized spherical gold nanoparticles grafted on Si(100) are probed by linear UV-vis, Fourier transform infrared and nonlinear infrared-visible vibrational sum/difference–frequency generation spectroscopies as a function of the nanoparticles surface coverage. Depending on the dipping time (5 min, 20 min, 1 h, and 24 h) in the colloidal solution, AFM imaging corroborates that the silicon surface coverage with gold nanoparticles increases, while the distance between neighbouring nanoparticles decreases, leading to their aggregation which dramatically impacts their optical properties. In the UV-vis reflectance spectra after the appearance of the 525-nm individual plasmonic band, a second broad band located at 660 nm and related to the gold nanoparticles aggregation on silicon rapidly dominates in intensity. Nonlinear vibrational spectroscopy is able to detect the specific vibration of the thiophenol molecules (3,055 cm−1) whatever the immersion time and at least down to 1 % of the substrate filling factor by the gold nanoparticles, overtaking the molecular sensitivity threshold of surface infrared and Raman spectroscopies on small gold nanostructures (17 nm) adsorbed on a semiconductor. Moreover, a quantitative analysis of the nonlinear vibrational fingerprint from 5 min to 24 h in the framework of the effective medium models of Maxwell-Garnett and Bruggeman illustrates the role played by the interband and the plasmonic properties of gold modulated by the silicon optical response. In this case, the sample reflectivity affects the molecular oscillator strength measured by nonlinear optical vibrational spectroscopy. For this latter technique, no coupling with the optical properties of aggregated AuNps is evidenced while the localized surface plasmon resonance excitation amplifies the molecular response.