Two medieval illuminated parchment scrolls of the Museo Diocesano of Bari (Italy), i.e., the Exultet I and the Benedictio ignis et fontis, were examined. Micro-samples of parchment were analyzed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) for the identification of collagen and its animal origin. Thanks to the overlapping folios, representing a unique situation for illuminated manuscripts, it was possible to sample tiny amounts of paint layers. A very small fraction was first investigated by pyrolysis-gas chromatography–mass spectrometry (Py-GC–MS), laying the way for an overview of all organic components. Detailed information on polysaccharides, and proteins and lipids were then attained by performing GC–MS and MALDI-MS analysis, respectively. Accordingly, the presence of paint binders based on egg white with the addition of some egg yolk was established in the Benedictio ignis et fontis, whereas in the Exultet I collagen and a fruit tree gum were identified, the latter probably due to a surface treatment of the entire scroll. The proposed multi-technique approach using easy sample pre-treatments on very small samples may shed a light on the medieval paint recipes and on the type of animal hides used for manufacturing this kind of precious parchment scrolls.