The so-called "Alligatoring" paint deterioration phenomenon was investigated through the study of four samples from O Cardeal D. Henrique recebendo a notícia da morte de D. Sebastião, painted in 1861 by the Portuguese painter Marciano Henriques da Silva. Attenuated Total internal Reflection Fourier Transform Infrared (ATR-FTIR) microscopy and Time-Of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS) imaging, complementary to Scanning Electron Microscopy Energy-dispersive X-Ray spectroscopy (SEM-EDX), were used to tackle the complexity of such paint systems and locate the distribution of organic/inorganic/hybrid components in the paint layers stratigraphy. While the use of asphalt/bitumen commonly associated with this peculiar paint deterioration, was hypothetised, its presence could not be confirmed nor denied with the methodological approach proposed. However, specific chemical compounds and paint layer structures were identified, both related to strong drying issues of the paint system. Most specifically, the evidence of a stable lead azelate layer together with lead and aluminium carboxylates present in all paint layers, combined with a paint technique with numerous paint layer superimposed and an excess of oil in the paint system can be pointed out as clues in the understanding of the degradation mechanisms.