This study investigates the suitability of using caffeine-treated and untreated black cherry (Prunus serotina Ehrh.) wood as a polylactide filler. Composites containing 10%, 20%, and 30% filler were investigated in terms of increasing the nucleating ability of polylactide, as well as enhancing its resistance to microorganisms. Differential scanning calorimetry studies showed that the addition of caffeine-treated wood significantly altered the crystallization behavior of the polymer matrix, increasing its crystallization temperature and degree of crystallinity. Polarized light microscopic observations revealed that only the caffeine-treated wood induced the formation of transcrystalline structures in the polylactide. Incorporation of the modified filler into the matrix was also responsible for changes in the thermal stability and decreased hydrophilicity of the material. Most importantly, the use of black cherry wood treated with caffeine imparted antifungal properties to the polylactide-based composite, effectively reducing growth of Fusarium oxysporum, Fusarium culmorum, Alternaria alternata, and Trichoderma viride. For the first time, it was reported that treatment of wood with a caffeine compound of natural origin alters the supermolecular structure, nucleating abilities, and imparts antifungal properties of polylactide/wood composites, providing promising insights into the structure-properties relationship of such composites.