Introduction: Biodeterioration is a big challenge for the preservation of cultural heritage objects and for the community’s safety, fostering the search for novel methods effective in removing microbial biofilms and subsequent biodeterioration. In this context, nanoparticles (NPs) are considered an interesting alternative, based on their unique physico-chemical and biological properties.Methods: The present study aimed to evaluate the antimicrobial efficiency of Ag, Au, Cu, and ZnO NPs against a significant number of filamentous fungi and bacterial strains isolated from wooden and stone cultural heritage objects from different Romanian regions, as well as from museum collections, with the final goal to establish their potential to develop novel preservation strategies, which have high efficiency and low ecotoxicity.Results: Six types of nanoparticles (NPs) based on Ag, Au, Cu, and ZnO were synthesized and characterized for their physico-chemical properties, ecotoxicity, and efficacy against 75 filamentous fungi and 17 bacterial strains isolated from wooden and stone cultural heritage objects (15th–19th century). The results showed that all synthetized NPs are homogeneous, demonstrating a good stabilizing coating, and have spherical or triangular shapes, with sizes between 9 and 25 nm. The highest antifungal efficiency has been recorded for Ag NPs, followed by Cu NPs and ZnO NPs, with the most susceptible strains being Aspergillus montevidensis, Penicillium commune, Penicillium corylophilum, Bacillus megaterium, and B. cereus. The Cu NPs and ZnO NPs decreased the capacity of microbial strains to adhere to the inert substratum. The influence of the tested NPs against enzyme/organic acid production varied depending on the NP types and by species.Conclusion: The obtained results are promising for the development of efficient and economical alternative solutions for heritage preservation, showing high antimicrobial activity against the prevalent fungal and bacterial strains involved in the biodeterioration of Romanian heritage objects.