Medieval wall paintings in the church of the monastery of St. John in Müstair (Switzerland) have been exposed to several fires over the last centuries. Non-invasive (hand-held-XRF) and microinvasive (PLM, SEM-EDX, XRPD, µ-Raman, and SERS) techniques were used to analyse 14 painted fragments from the Romanesque (c. 1200 CE) painting cycle recovered from the attic of the church above younger Gothic vaulting in order to study the microstratigraphy of the painted surfaces and determine alterations and newly formed products, with the aim of understanding if the darkening was directly attributable to contact with fire. Scientific, historical, and bibliographical research have shown that alteration processes in the pigments from these paintings are not directly linked with fires, except possibly for two lead-based painted fragments. This indicates that the action of the historically documented fires in the church was not uniform and did not affect all areas of the paintings equally.