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The mycobiome of the cave Church of Sts. Peter and Paul, housing the peculiar fresco painting of “The Bald-headed Jesus”, was analyzed via culture-dependent and -independent methods. Salt efflorescence, colored patinas, and biofilm, as well as biopitting, discolorations, and fruiting bodies of wood-decay fungi were observed on surfaces within the church. Microscopic analyses showed an abundance of fungal structures, i.e., conidiophores, conidia, chlamydospores, and ascospores. The estimated values of the contamination classified all surfaces as the “Danger zone”. A total of 24 fungi from 17 genera were determined as part of the culturable mycobiome, with a dominance of <i>Ascomycota</i> of genera <i>Penicillium</i>. Biodegradative profiles analyzed via plate assays demonstrated positive reactions for 16 isolates: most commonly acid production (8), followed by pigment production and ligninolytic activity (6), protein degradation (5), cellulolytic activity (3) and carbonate dissolution (2). Metabarcoding analysis showed a dominance of <i>Ascomycota</i> in all samples (79.9–99.7%), with high relative abundance documented for <i>Hypoxylon fuscopurpureum</i> on the iconostasis and unclassified <i>Mycosphaerellaceae</i> family within order <i>Capnodiales</i> on fresco and stone, as well as moderate relative abundance for unclassified <i>Dothideomycetes</i>, <i>Botryolepraria lesdainii</i>, <i>Verrucaria</i> sp. and <i>Cladosporium</i> sp. on stone walls. The used set of integrative methods pointed out species of genus <i>Neodevriesia</i> and <i>H. fuscopurpureum</i> as the main deteriogenic agents of fresco and iconostasis surfaces, respectively.