Polymer composites with renewable lignocellulosic fillers, despite their many advantages, are susceptible to biodegradation, which is a major limitation in terms of external applications. The work uses an innovative hybrid propolis-silane modifier in order to simultaneously increase the resistance to fungal attack, as well as to ensure good interfacial adhesion of the filler–polymer matrix. Polypropylene composites with 30% pine wood content were obtained by extrusion and pressing. The samples were exposed to the fungi: white-rot fungus Coriolus versicolor, brown-rot fungus Coniophora puteana, and soft-rot fungus Chaetomium globosum for 8 weeks. Additionally, biological tests of samples that had been previously exposed to UV radiation were carried out, which allowed the determination of the influence of both factors on the surface destruction of composite materials. The X-ray diffraction, attenuated total reflectance–Fourier transform infrared spectroscopy, and mycological studies showed a significant effect of the modification of the lignocellulose filler with propolis on increasing the resistance to fungi. Such composites were characterized by no changes in the supermolecular structure and slight changes in the intensity of the bands characteristic of polysaccharides and lignin. In the case of systems containing pine wood that had not been modified with propolis, significant changes in the crystalline structure of polymer composites were noted, indicating the progress of decay processes. Moreover, the modification of the propolis-silane hybrid system wood resulted in the inhibition of photo- and biodegradation of WPC materials, as evidenced only by a slight deterioration in selected strength parameters. The applied innovative modifying system can therefore act as both an effective and ecological UV stabilizer, as well as an antifungal agent.