Surface plasmon resonance measurements and magnetic characterization studies have been carried out for two types of thiol-capped gold nanoparticles (NPs) with similar diameters between 2.0 and 2.5 nm and different organic molecules linked to the sulfur atom: dodecanethiol and tiopronin. In addition, Au NPs capped with tetraoctyl ammonium bromide have also been included in the investigation since such capping molecules weakly interact with the gold surface atoms and, therefore, this system can be used as a model for naked gold NPs; such particles presented a bimodal size distribution with diameters around 1.5 and 5 nm. The plasmon resonance is non-existent for tiopronin-capped NPs, whereas a trace of such a feature is observed for NPs covered with dodecanethiol molecules and a bulk-like feature is measured for NPs capped with tetralkyl ammonium salts. These differences would indicate that the modification of the surface electronic structure of the Au NPs depends on the geometry and self-assembling capabilities of the capping molecules and on the electric charge transferred between Au and S atoms. Regarding the magnetization, dodecanethiol-capped NPs have a ferromagnetic-like behaviour, while the NPs capped with tiopronin exhibit a paramagnetic behaviour and tetralkyl ammonium-protected NPs are diamagnetic across the studied temperature range; straight chains with a well-defined symmetry axis can induce orbital momentum on surface electrons close to the binding atoms. The orbital momentum not only contributes to the magnetization but also to the local anisotropy, giving rise to permanent magnetism. Due to the domain structure of the adsorbed molecules, orbital momentum is not induced for tiopronin-capped NPs and the charge transfer only induces a paramagnetic spin component.