Deposition of gold nanoparticles (AuNPs) on a solid substrate followed by oxygen plasma treatment is a commonly used protocol for surface functionalization. Surprisingly, the effect of the deposition process and oxygen plasma on the morphology of the AuNPs is usually overlooked in research. Here, we investigated morphological changes caused by (i) adsorption of small ligand-capped AuNPs (5 nm in diameter) onto a silicon substrate and (ii) subsequent oxygen plasma treatment. AuNPs coated with positively and negatively charged as well as uncharged ligands have been investigated. It is found that upon the adsorption the AuNPs undergo plastic deformations and their shapes can be approximated by spherical caps. The degree of the deformation depends strongly on the AuNP coating. During the plasma treatment the AuNPs behave like droplets of a non-wetting liquid, exhibiting the ability to move and merge. We argue that the AuNP coarsening is dominated by the diffusion coalescence mechanism and show that time evolution of the surface AuNP density follows the Smoluchowski coagulation equation. The diffusivity of the AuNP scales with its mass as D(m) m−α with α = 2.6.