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The functionalization of inorganic surfaces by organic functional molecules is a viable and promising method towards the realization of novel classes of biosensing devices. The proper comprehension of the chemical properties of the interface, as well as of the number of active binding sites for bioreceptor molecules are characteristics that will determine the interaction of the sensor with the analyte, and thus its final efficiency. We present a new and reliable surface functionalization route based on supersonic molecular beam deposition (SuMBD) using 2,6-naphthalene dicarboxylic acid as a bi-functional molecular linker on the chemically inert silicon nitride surface to further allow for stable and homogeneous attachment of biomolecules. The kinetically activated binding of the molecular layer to silicon nitride and the growth as a function of deposition time was studied by X-ray photoelectron spectroscopy, and the properties of films with different thicknesses were investigated by optical and vibrational spectroscopies. After subsequent attachment of a biological probe, fluorescence analysis was used to estimate the molecular layer’s surface density. The successful functionalization of silicon nitride surface via SuMBD and the detailed growth and interface analysis paves the way for reliably attaching bioreceptor molecules onto the silicon nitride surface.