In this work, we applied scanning electron microscopy (SEM), microanalysis and Raman spectroscopy to study the fungi inhabiting a richly illuminated parchment document and the damage induced by their activity. To that aim, we collected samples of fungal mycelium from the deteriorated areas on a removable adhesive tape specifically intended for lifting fungi without damaging the support. SEM analysis of the adhesive tape samples showed the co-occurrence of several species of fungi. One strain closely resembling Acremonium species was observed only in the tape micrographs but no agar cultures were obtained. Its fungal structures showed the production of abundant oxalates with an outstanding leaching of the calcium-based materials of parchment (typically manufactured with gypsum and lime). Needle-like crystals of calcium oxalate produced by the fungus forming a uniform and quite regular grid around conidial slimy heads were documented. As a result, the areas affected by moulds were weakened, stained and characterised by a powdery patina rich in calcium. Confocal μ-Raman confirmed the presence of oxalates while EDS showed the presence of calcium in crystals. We conclude that the defacement of the parchment was due to both collagenolytic activity, and to the biotransformation of calcium-based minerals by fungi.