Plasma polymerization of 3-aminopropyl-triethoxysilane (APTES) in microwave late afterglow was studied. First, sol-gel polymerized APTES was prepared and characterized by ATR–FTIR and XPS. The results obtained were used as a model to define the nature of nitrogen containing groups in the plasma polymer layers. It is shown that the variation of process gas mixture gives the possibility to tailor the chemical composition of the coatings. We show that nitrogen can be present in the thin films as amines, amides, imines or oximes. The analysis of the gas phase composition by OES during the deposition process was realized and based on the correlations established between OES results and thin film compositions, some assumptions on the chemical mechanisms involved in the gas phase are discussed.