Different Portuguese limestones-Encarnadão, Amarelo de Negrais, Lioz and Gresoso-have been widely used as building materials and ornamental stones in the architecture of Lisbon (Portugal) area.The aim of the study of those materials was focused on fire-induced stone damage, mainly on identifying the thermal transformations of clay minerals and iron oxides-oxyhydroxides. Taking into account an applied component to the cultural heritage, a special attention was given to one of the most ancient Portuguese monuments — Lisbon Cathedral, specifically its cloister that was severely damaged by a fire that occurred right after the 1755 earthquake.A set of samples collected from outcrops were studied and subjected to artificial heating. The results were compared with those obtained from samples collected in the monument. XRD, SEM-EDS and 57Fe Mössbauer spectroscopy were used. The < 2 µm fraction varies significantly between unheated (outcrop samples) and artificially heated samples, particularly in relation to iron oxides-oxyhydroxides. Kaolinite is the dominant clay mineral, followed by illite and smectite. Goethite is the iron oxyhydroxide characteristic of all studied lithotypes both in unheated samples and samples artificially heated to 250 °C. Encarnadão is the exception presenting hematite in those conditions. As firing temperature increases (300 °C–600 °C) disordered hematite appears at the expense of goethite, and smectite is no longer detected. Mössbauer spectra further reveal that Fe2+ in silicate minerals is fully oxidized at 600 °C but remains in the carbonate structure up to this temperature. The SEM-EDS analyses show that 2:1 clay minerals have Si and Al as main cations and minor amounts of K and Fe. It also shows that all the clay minerals and Fe-rich particles are always associated to the limestone porosity.. The present results show that the clay minerals, namely illite–smectite mixed-layer and smectite, can be used as indicators of stone provenance used in Lisbon Cathedral Cloister as well as fingerprints of the temperature achieved during the fire of Lisbon Cathedral that most likely was not higher than 350 °C.