Abstract This paper accounts for the diagnostic campaign aimed at understanding the phenomenon of black stains appeared on the passepartout close to the margins of Folio 843 of Leonardo da Vinci’s Codex Atlanticus . Previous studies excluded microbiological deterioration processes. The study is based on a multi-analytical approach, including non-invasive imaging measurements of the folio, micro-imaging and synchrotron spectroscopy investigations of passepartout fragments at different magnifications and spectral ranges. Photoluminescence hyperspectral and lifetime imaging highlighted that black stains are not composed of fluorescent materials. μATR-FTIR imaging of fragments from the passepartout revealed the presence of a mixture of starch and PVAc glues localized only in the stained areas close to the margin of the folio . FE-SEM observations showed that the dark stains are localized inside cavities formed among cellulose fibers, where an accumulation of inorganic roundish particles (∅100–200 nm in diameter size), composed of Hg and S, was detected. Finally, by employing synchrotron μXRF, μXANES and HR-XRD analyses it was possible to identify these particles as metacinnabar (β-HgS). Further research is needed to assess the chemical process leading to the metacinnabar formation in the controlled conservation condition of Leonardo’s Codex .