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Vibrational spectroscopy is the most effective, efficient and informative method of structural analysis of amorphous materials with silica matrix and, therefore, an indispensable tool for examining silicon oxycarbide-based amorphous materials (SiOC). The subject of this work is a description of the modification process of SiOC glasses with phosphate ions based on the structural examination including mainly Infrared and Raman Spectroscopy. They were obtained as polymer-derived ceramics based on ladder-like silsesquioxanes synthesised via the sol-gel method. With the high phosphate's volatility, it was decided to introduce the co-doping ions to create [AlPO4] and [BPO4] stable structural units. As a result, several samples from the SiPOC, SiPAlOC and SiPBOC systems were obtained with various quantities of the modifiers. All samples underwent a detailed structural evaluation of both polymer precursors and ceramics after high-temperature treatment with Fourier-transformed infrared spectroscopy (FTIR), Raman spectroscopy, X-ray diffraction (XRD) and magic angle spinning nuclear magnetic resonance (MAS-NMR). Obtained results proved the efficient preparation of desired materials that exhibit structural parameters similar to the unmodified one. They were X-ray-amorphous with no phase separation and crystallisation. Spectroscopic measurements confirmed the presence of the crucial Si-C bond and how modifying ions are incorporated into the SiOC network. It was also possible to characterise the turbostratic free carbon phase. The modification was aimed to improve the bioperformance of the materials in the context of their future application as bioactive coatings on metallic implants.