A novel approach of combining conventional infrared spectroscopy (IR) and atomic force microscopy (AFM) is presented to better understand the behavior of a drug adsorbed on a metal substrate at the nanoscale level. Tip-enhanced infrared nanospectroscopy (TEIRA) was used for the first time to investigate Lu AA33810, a selective brain-penetrating Y5 receptor antagonist, after immobilization on gold nanoparticles (GNPs). Here, a gold coated AFM tip and gold substrate were used to obtain the near-field electromagnetic field trapping effect. Because of the huge signal enhancement, it was possible to obtain the spectral information regarding the self-assembled monolayer of the investigated molecule. The effect of two orthogonal polarizations (p- and s-polarization modulations) of the excitation laser beam on the spectral patterns is also discussed. The results show that there is a strong relationship between the state of polarization of the incident radiation and the relative infrared band intensities. Another factor affecting the observed spectral differences is the topology of the metal substrate, which may result in the induction of a cross-polarization effect. The performed analysis indicates that the C–C bond from the cyclohexyl group is oriented almost parallel to the metal surface. Conversely, the p- and s-polarized spectral variations suggest that the O=S=O angle is high enough to enable the simultaneous interaction of both oxygen atoms with the GNPs.