The interaction of nitrogen, oxygen, and hydrogen plasmas with spin-coated arrays of colloidal cobalt–platinum particles was investigated with a large variety of microscopic and spectroscopic techniques. It could be demonstrated that the organic ligands of the nanoparticles can be completely removed. Yet, due to the short (∼1.6 nm) interparticle distances within the layers, strong degradation and sintering effects are observed after hydrogen and nitrogen plasma treatments. In the case of oxygen plasma, the shape and size of the individual particles are unaffected and can be preserved, even if a short hydrogen plasma is subsequently applied to reduce the particles back to their metallic state. Nevertheless, the mesoscopic order of the particle arrays is slightly decreased as observed by the breakup of larger ordered areas into smaller domains forming island–trench structures. Probing the surface chemistry of the particles with temperature programmed desorption, a rather complex surface chemistry is found to result from the plasma treatments. The first TPD spectrum after the cleaning process with oxygen and subsequent hydrogen plasmas reveals that the particles are loaded with adsorbed and implanted hydrogen. After removal of this hydrogen, subsequent TPD spectra using CO as a probe molecule, show broad signals between 190 and 360 K pointing to nonmetallic surface properties. While the platinum was found to be completely reduced, XPS measurements reveal a remaining fraction of oxidic cobalt species which are enriched at the surface. Thus, although the structure of the close-packed Co–Pt nanoparticle arrays can be qualitatively preserved during plasma-based ligand removal, the treatment leads to a complex materials system the chemical properties of which are influenced by the particle components, the substrate, and the plasma media.