Moulds inhabiting mineral-based materials may cause their biodeterioration, contributing to inestimable losses, especially in the case of cultural heritage objects and architectures. Fungi in mouldy buildings may also pose a threat to human health and constitute the main etiological factor in building related illnesses. In this context, research into novel compounds with antifungal activity is of high importance. The aim of this study was to evaluate the antifungal activity of polyoxometalate-ionic liquids (POM-ILs) and their use in the eradication of moulds from historical brick. In the disc diffusion assay, all the tested POM-ILs inhibited growth of a mixed culture of moulds including Engyodontium album, Cladosporium cladosporioides, Alternaria alternata and Aspergillus fumigatus. These were isolated from the surfaces of historical brick barracks at the Auschwitz II-Birkenau State Museum in Oświęcim, Poland. POM-IL coatings on historical brick samples, under model conditions, showed that two compounds demonstrated very high antifungal activity, completely limiting mould growth and development. The antifungal activity of the POM-ILs appeared to stem from their toxic effects on conidia, as evidenced by environmental scanning transmission electron microscopy observations. The results herein indicated that POM-ILs are promising disinfectant materials for use not only on historical objects, but probably also on other mineral-based materials.