Thin film deposition with atmospheric pressure plasmas is highly interesting for industrial demands and scientific interests in the field of biomaterials. However, the engineering of high-quality films by high-pressure plasmas with precise control over morphology and surface chemistry still poses a challenge. The two types of atmospheric-pressure plasma depositions of organosilicon films by the direct and indirect injection of hexamethyldisiloxane (HMDSO) precursor into a plasma region were chosen and compared in terms of the films chemical composition and morphology to address this. Although different methods of plasma excitation were used, the deposition of inorganic films with above 98% of SiO2 content was achieved for both cases. The chemical structure of the films was insignificantly dependent on the substrate type. The deposition in the afterglow of the DC discharge resulted in a soft film with high roughness, whereas RF plasma deposition led to a smoother film. In the case of the RF plasma deposition on polymeric materials resulted in films with delamination and cracks formation. Lastly, despite some material limitations, both deposition methods demonstrated significant potential for SiOx thin-films preparation for a variety of bio-related substrates, including glass, ceramics, metals, and polymers.