In this work, pulsed phase thermography (PPT), principal component thermography (PCT), and partial least squares thermography (PLST) techniques were applied in order to detect the masonry texture, as well as to map the subsurface damages formed beneath three different mural paintings. The latter were inspected after the 2009 earthquake, i.e., the seismic event that devastated L’Aquila City (Italy) and its surroundings. The mural supports explored by infrared thermography (IRT) are constituted by a single leaf, and the sides of the inspected paintings are confined by marble frames or by buried horizontal and vertical structures. Hence, the analyzed objects can be considered as monolithic structures. IRT can help to understand the masonry morphology, e.g. if there exist structural continuity between the arriccio layer (the first coat of plaster) and the support. In the present case, the heating phase was provided by lamps or propane gas and feature detection was enhanced by advanced signal processing. A comparison among the results is presented. Two of the three objects analyzed, painted by the art masters Serbucci and Avicola, are preserved inside Santa Maria della Croce di Roio Church in Roio Poggio (L’Aquila, Italy); they were executed on two masonries built in different periods. The last one was realized in Montorio al Vomano (Teramo, Italy) on the internal cloister of the Zoccolanti’s Church (undated). The villages are separated by 50 km as the crow flies. Finally, near-infrared reflectography (NIRR) technique was also used to investigate the condition of the painting layer.