Gold nanoparticles with an average particle size below 3 nm have been synthesized and stabilized with different thiol-derivatized molecules for studying the influence of the capping molecule on the magnetic behavior. Thiolated-alkane chains with different lengths as well as a thiol-containing biomolecule (tiopronin) have been selected as protecting shells for the synthesized NPs. Magnetic characterization indicates that the appearance of a ferromagnetic-like behavior is related not only with the formation of Au-S bonds linking the protective molecules to the nanoparticle surface but also with the formation of the nanoparticle itself as well as with the geometry of the capping molecule. The later seems to determine whether the protective monolayer shell is ordered or not. The simultaneous presence of Au-Au and Au-S bonds together with a reduced particle diameter, and the formation of an ordered monolayer protective shell, have been proved to be key parameters for the ferromagnetic-like behavior exhibited by thiol-functionalized gold NPs.