The article presents characteristics of wood/polypropylene composites, where the wood was treated with propolis extract (EEP) and innovative propolis-silane formulations. Special interest in propolis for wood impregnation is due to its antimicrobial properties. One propolis-silane formulation (EEP-TEOS/VTMOS) consisted of EEP, tetraethyl orthosilicate (TEOS), and vinyltrimethoxysilane (VTMOS), while the other (EEP-TEOS/OTEOS) contained EEP, tetraethyl orthosilicate (TEOS), and octyltriethoxysilane (OTEOS). The treated wood fillers were characterized by Fourier transform infrared spectroscopy (FTIR), atomic absorption spectrometry (AAS), and X-ray diffraction (XRD), while the composites were investigated using differential scanning calorimetry (DSC), X-ray diffraction (XRD), and optical microscopy. The wood treated with EEP and propolis-silane formulations showed resistance against moulds, including Aspergillus niger, Chaetomium globosum, and Trichoderma viride. The chemical analyses confirmed presence of silanes and constituents of propolis in wood structure. In addition, treatment of wood with the propolis-silane formulations produced significant changes in nucleating abilities of wood in the polypropylene matrix, which was confirmed by an increase in crystallization temperature and crystal conversion, as well as a decrease in half-time of crystallization parameters compared to the untreated polymer matrix. In all the composites, the formation of a transcrystalline layer was observed, with the greatest rate recorded for the composite with the filler treated with EEP-TEOS/OTEOS. Moreover, impregnation of wood with propolis-silane formulations resulted in a considerable improvement of strength properties in the produced composites. A dependence was found between changes in the polymorphic structures of the polypropylene matrix and strength properties of composite materials. It needs to be stressed that to date literature sources have not reported on treatment of wood fillers using bifunctional modifiers providing a simultaneous effect of compatibility in the polymer-filler system or any protective effect against fungi.