The adsorption of a globular protein on chemically well controlled surfaces was investigated in order to correlate its orientation to the surface properties. To this end, three different alkyl thiols, differing by their end group (−COOH, −CH3, and −NH2), were used to build up self-assembled monolayers (SAMs) on gold substrates. β-Lactoglobulin (βLG) was then adsorbed on these SAMs by immersion in a phosphate buffer solution. The surface modification with alkyl thiols and the subsequent adsorption of proteins were characterized ex situ by polarization modulated infrared reflection-absorption spectroscopy (PM-IRRAS) and X-ray photoelectron spectroscopy (XPS). The adsorption behavior of proteins was also monitored in situ using quartz crystal microbalance with dissipation measurements (QCM-D). Direct evidence regarding the protein orientation in the adsorbed state was obtained by means of time-of-flight secondary ion mass spectrometry (ToF-SIMS). Principal component analysis (PCA), performed on the ToF-SIMS results, enables to separate the samples and shows that the proteins display different distributions of amino acids at the surface depending on the conditioning thiol layer. Our results revealed that the adsorption mode of the protein is influenced by the thiol end groups, and specific orientations of the protein on the surface are proposed for the different substrates.