The influence of the number of molecule–metal interactions on the surface-enhanced Raman scattering (SERS) spectroscopy of 1,4-benzenedithiol (BDT) was investigated. For this purpose, a series of SERS-active samples were prepared featuring one or two molecule–metal interfaces. Molecules were adsorbed on the surface of a rough Au substrate, or sandwiched between Au nanoparticles (NPs) and a flat Au(111) substrate in a “sphere–plane” disposition. In the presence of the Au surface(s), vibrational energy and intensity of the SERS spectra differs significantly from the bulk. Molecule–metal charge transfer upon chemisorption weakens intramolecular bonds, resulting in the observed red shift of the breathing and CC stretching modes. This effect was found to be more pronounced for samples with multiple molecule–metal interfaces. In addition, the SERS spectra of BDT featured additional b 2 signals not present in the bulk spectra. Chemical enhancement of the b 2 modes takes place by means of photoinduced charge transfer from an occupied molecular orbital to an unoccupied metal orbital. Analysis of the normalized SERS intensity revealed a larger scattering enhancement for the samples with a sphere–plane disposition arising from the stronger electromagnetic enhancement effect via plasmonic localization of optical fields. Complementary studies on 4-aminobenzenethiol support these findings.