The fungal community of biodeteriorated 17th century mural paintings within the nave and altar portion of the old Church of the Holy Ascension (Veliki Krcimir, Nisava District, Serbia) has been studied via an array of microscopic analyses in order to detect actively growing fungi and assess their potential damage to the painted layer and mortar. In situ microscopy, performed with portable microscopes, together with optical and scanning electron microscopy, has revealed impairments of the painted layer in the form of cracks and biopitting, along with surface salt deposits and hidden, symptomless fungal growth. Various structures, such as fully developed fruiting bodies and melanized mycelia, clusters of microcolonial fungi and lichen soredia, as well as a conidial apparatus and numerous conidia in mass have been observed, all attesting to the presence of actively growing fungal community on the surface of the painted layer and in the interspaces between the painted layer and mortar. Based on the observed reproductive structures, the main agents of biodeterioration have been identified as fungi of Chaetomium and Cladosporium genera. The documented deterioration symptoms are most likely due to hyphal penetration and formation of fruiting bodies and other fungal structures.