In this study, functional nanocoatings for waterproof footwear leather materials were investigated by chemical plasma polymerization by implanting and depositing the organosilicon compound hexamethyldisiloxane (HMDSO) using a low-pressure plasma system. To this end, the effect of monomers on leather plasma deposition time was evaluated and both the resulting plasma polymers and the deposited leather samples were characterised using different experimental techniques, such as: Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM). In addition, leather samples were tested by standard tests for color change, water resistance, surface wetting resistance and dynamic water contact angle (DWCA). The resulting polysiloxane polymers exhibited hydrophobic properties on leather. Furthermore, these chemical surface modifications created on the substrate can produce water repellent effects without altering the visual leather appearance and physical properties. Both plasma coating treatments and nanocoatings with developed water-repellency properties can be considered as a more sustainable, automated and less polluting alternative to chemical conventional processing that can be introduced into product-finishing processes in the footwear industry.