Micro-Infrared Spectroscopy (mSR-FTIR) and X-ray diffraction (mSR-XRD) with synchrotron light, Gas Chromatography/Mass Spectrometry (CG/MS), Optical Microscopy (OM) and Scanning Electron Microscopy (SEM/EDS) were used to identify and obtain the distribution of complex mixtures of calcium salts of low molecular weight organic acids (LMWOA) in micro-layered micro-samples. Filamentous fungi produce LMWOA that can react with metal cations producing stable salts. These substances were found in the dark spots covering the surfaces of Saint Michael's Chapel wall paintings of the Royal Monastery of Pedralbes in Barcelona linking them to old fungi activity. The presence of glycerol likewise related to the fungi activity is also identified in the layers.