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Nitridation of different materials using ion implantation is of considerable interest for many applications. As electronic components, oxynitride (SiOxNy) layers exhibit beneficial properties such as precise compositional variability, refractive index tunability, oxidation resistance, and low mechanical stress. In the present study we investigate nanoscale SiOxNy synthesized using ion implantation methods. To introduce N+ ions into a shallow Si subsurface region, both conventional ion beam implantation and plasma immersion ion implantation with subsequent high-temperature treatment in dry O2 are used. The optical and morphological properties and chemical bonding of formed SiOxNy layers were studied by applying spectroscopic ellipsometry in the range of VIS-Near IR (SE) and IR (IR-SE), Raman spectroscopy and Atomic Force Microscopy (AFM). Monte Carlo modeling of implant profiles contributed to understanding physical and chemical processes and predicted different influences of the incorporated N+ ions on the oxidation mechanism, confirmed by the thickness dependence of SiOxNy/Si layers obtained from the SE data analysis. IR-SE spectral analysis established the formation of Si-O, Si-N, Si-N-O and Si-Si chemical bonds in the grown layers. The occurrence of amorphization of the Si crystal lattice due to incorporation of high-energy N+ ions into the Si lattice is confirmed by the Raman and ellipsometry results. The free Si atoms can congregate, forming nanocrystalline clusters. AFM imaging revealed that both implantation methods left the surface of the resulting SiOxNy layers considerably smooth with similar roughness parameter values. The results of the studies imply that the technological approaches used allow the production of high-quality nanoscale silicon oxynitride films with appropriate tunable composition and properties for possible application in advanced electronic devices for nanoelectronics, optoelectronics and sensor applications.