This research centered on enhancing the mechanical properties of sustainable composite materials made from short flax fibers. Challenges associated with fiber–matrix adhesion and moisture absorption were systematically addressed. A water–alginate pre-treatment, combined with plasma modification, was employed to stabilize the fibers, ensuring their optimal preparation and improved compatibility with biopolymers. A thorough investigation of the effect of the plasma modulation using a duty cycle (DC) was conducted, and extensive physicochemical and mechanical analyses were performed. These efforts revealed conditions that preserved fiber integrity while significantly improving surface characteristics. Techniques such as optical emission spectroscopy (OES), Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), and Dynamic Mechanical Analysis (DMA) were utilized, providing a comprehensive understanding of the transformations induced by the plasma treatment. The findings underscored the critical role of alginate and precise plasma settings in enhancing the mechanical properties of the composites. Ultimately, this study made a substantial contribution to the field of eco-friendly materials, showcasing the potential of short flax fibers in sustainable composite applications and setting the stage for future advancements in this area.