Grape seeds (GS), wine lees (WL), and grape pomace (GP) are common winery by-products, used as bio-fillers in this research with two distinct biopolymer matrices—poly(butylene adipate-co-terephthalate) (PBAT) and polybutylene succinate (PBS)—to create fully bio-based composite materials. Each composite included at least 30 v% bio-filler, with a sample reaching 40 v%, as we sought to determine a composition that could be economically and environmentally effective as a substitute for a pure biopolymer matrix. The compounding process employed a twin-screw extruder followed by an injection molding procedure to fabricate the specimens. An acetylation treatment assessed the specimen’s efficacy in enhancing matrix–bio-filler affinity, particularly for WL and GS. The fabricated bio-composites underwent an accurate characterization, revealing no alteration in thermal properties after compounding with bio-fillers. Moreover, hygroscopic measurements indicated increased water-affinity in bio-composites compared to neat biopolymer, most significantly with GP, which exhibited a 7-fold increase. Both tensile and dynamic mechanical tests demonstrated that bio-fillers not only preserved, but significantly enhanced, the stiffness of the neat biopolymer across all samples. In this regard, the most promising results were achieved with the PBAT and acetylated GS sample, showing a 162% relative increase in Young’s modulus, and the PBS and WL sample, which exhibited the highest absolute values of Young’s modulus and storage modulus, even at high temperatures. These findings underscore the scientific importance of exploring the interaction between bio-fillers derived from winery by-products and three different biopolymer matrices, showcasing their potential for sustainable material development, and advancing polymer science and bio-sourced material processing. From a practical standpoint, the study highlighted the tangible benefits of using by-product bio-fillers, including cost savings, waste reduction, and environmental advantages, thus paving the way for greener and more economically viable material production practices.