Significant progress has been made in recent years in the use of atmospheric pressure plasma techniques for surface modification. This research focused on the beneficial effects of these processes on natural by-products, specifically those involving natural fiber-based materials. The study explored the deposition of hydrophobic organosilicon-like thin films onto flax fibres through plasma-enhanced chemical vapour deposition (PECVD), using tetramethylcyclotetrasiloxane (TMCTS) as the precursor. After the successful deposition of hydrophobic organosilicon-like thin films onto the flax fibres, polylactic acid (PLA) composite materials were fabricated. This fabrication process sets the stage for an in-depth analysis of the modified materials. Subsequently, these flax fabrics were subjected to meticulous characterization through scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), and contact angle measurements. The results demonstrated successful TMCTS deposition on the surface which led to a complete hydrophobization of the flax fibers. Mechanical tests of the PLA/flax fibre composites revealed a significant improvement in load transfer and interfacial compatibility following the surface modification of the flax fibres. This improvement was attributed to the enhanced adhesion between the modified fibres and the PLA matrix. The findings highlight the potential of TMCTS-based PECVD as a practical surface modification technique, effectively enhancing the mechanical properties of PLA/flax fibre composites. These developments open exciting possibilities for sustainable and high-performance composite materials in various industries.