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Silver nanoparticles (AgNPs) exert profound physicochemical, biological, and antimicrobial properties, therefore, they have been extensively studied for a variety of applications such as food packaging and cultural heritage protection. However, restrictions in their stability, aggregation phenomena, and toxicity limit their extensive use. Hence, the use of functional substrates that promote the silver nanoparticles’ growth and allow the formation of uniform-sized, evenly distributed, as well as stable nanoparticles, has been suggested. This study reports on the fabrication and the characterization of hydrophilic polymer spheres including nanoparticles with intrinsic antifungal properties. Poly (methacrylic acid) microspheres were synthesized, employing the distillation precipitation method, to provide monodisperse spherical substrates for the growth of silver nanoparticles, utilizing the co-precipitation of silver nitrate in aqueous media. The growth and the aggregation potential of the silver nanoparticles were studied, whereas the antifungal activity of the produced nanostructures was evaluated against the black mold-causing fungus Aspergillus niger. The produced structures exhibit dose-dependent antifungal activity. Therefore, they could potentially be employed for the protection and preservation of cultural heritage artifacts and considered as new agents for food protection from fungal contamination during storage.