The interaction of hydrogen with gold nanoparticles (Au NPs) and gold thin films also functionalized with thiols is investigated. Au NPs deposited on silicon substrates by radio frequency sputtering of a gold target and gold thin films have been exposed to a remote H2 plasma and subsequently functionalized by the aromatic (4-methoxyterphenyl-3″,5″-dimethanethiol) and aliphatic (dodecanethiol) thiols. The impact of hydrogenation on changes of the charge on gold surfaces and nanoparticles, on the kinetics of the thiol self-assembled monolayer (SAM) formation, and on the density of the resulting SAMs has been investigated combining spectroscopic ellipsometry (SE), Raman spectroscopy, and surface potential Kelvin probe microscopy (SP-KPM) in conjunction with noncontact atomic force microscopy (AFM). We found that remote H2 plasma pretreatments of gold surfaces are effective in improving thiolate adsorption, making SAMs more uniform and densely packed. We also demonstrate that hydrogenation of nanoparticles improves stability of thiol functionalized Au NPs, avoiding their aggregation. Additionally, we demonstrate that a remote H2 plasma processing is also effective in the selective removal of the carbon chain and of sulfur atoms from gold surfaces, therefore allowing tailoring of their optical and chemical properties.