In the present paper, we show an exhaustive microstructural characterization of thiol-capped gold nanoparticles (NPs) with two different average particle sizes. These samples are compared with the polymer-like Au(I) phase formed as a precursor during the synthesis of the thiol-capped gold NPs. The set of analysed samples shows different microstructures at the nanoscale with different proportions of Au atoms bonded either to S or to Au atoms. It has been experimentally shown that the presence of a ferromagnetic-like behaviour is associated to the formation of NPs with simultaneous presence of Au–Au and Au–S bonds. In order to explain such magnetic behaviour a possible model is proposed based on the spin–orbit coupling so that localized charges and/or spins (Au–S bonds) can trap conduction electrons (Au–Au bonds) in orbits. XAS facilities at BM29 in ESRF and the technical support from G.L. Ciatto are acknowledged. Financial support from the Spanish MEC (NAN2004-09125-C07) and “Junta de Andalucía” is also acknowledged. E. Guerrero thanks the Spanish MEC for financial support. Peer reviewed