A combined experimental–theoretical study of quercetin adsorbed on a silica surface has been carried out in order to investigate the specific nature of their interaction. By means of an accurate hybrid functional PBE-D* approach, inclusive of dispersion interactions through the empirical D* Grimme’s term, the energetics of various configurations has been evaluated. IR spectra of the most probable ones, determined on the basis of thermodynamics considerations, have been simulated and compared to ad hoc measured spectra. A detailed classification of the peaks is proposed which sheds light onto some cloudy parts of the experimental IR spectra assignments. The most notable feature of our results is the extended and enhanced hydrogen-bonds network which is formed throughout the surface-molecule aggregate, thanks to the molecule acting as a bridge among the hydrogen bonds already present on the pristine silica surface.