Thin layers of SiOxCy (y = 4−x and 3 ≤ x ≤ 4) were applied using a cold atmospheric plasma torch on glass substrates. The aim was to investigate using Atomic Force Microscopy (AFM), X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (Tof-Sims) the influence of the gases used on the morphology and composition of the deposits. A hexamethyldisilane (HMDS) precursor was injected in post-discharge in an air or nitrogen plasma using a carrier gas (air or nitrogen) and was applied on the substrate previously pre-treated by an air or nitrogen plasma. The carrier gas and plasma gas flows and the distance between the substrate and the plasma torch, the scanning speed, and the precursor flows were kept constant during the study. The gas used during activation pre-treatment showed no particular influence on the characteristics of the deposit. When air is used both as plasma and carrier gas, the coating layer is thicker (96 nm) than when nitrogen is used (64 nm). It was also evidenced that the gas carrying the precursor has little influence on the hydrophobicity of the coating, contrary to the plasma gas. The latter significantly influences the surface characteristics of the coatings. When air is used as plasma gas, a compact coating layer is obtained and the surface has a water contact angle (WCA) of 82°. When nitrogen is used, the deposit is more hydrophobic (WCA of 100°) and the deposit morphology is different. This increase in hydrophobicity could be correlated to the increase of Sisingle bondOsingle bondC bonds in the upper surface layers evidenced by XPS analyzes. This observation was then confirmed by Tof-Sims analyzes carried out on these thin layers. A uniform distribution of Carbons in the siloxane coating could also be observed using Tof-Sims 2D reconstruction images of cross sections of the deposited layers.