This paper deals with the development of a multidisciplinary study on the current state of conservation of the facade of the Arciprestal Church of Santa María de Morella (Castellón, Spain), a work of the Gothic period of great historical and artistic value. The aim of this diagnosis was to undertake the preventive conservation actions required and increase the knowledge about the conservation of paintings on stones. During the diagnosis scanning, electron microscopy was demonstrated to be a valuable analytical method for wall paintings on stone. The facade, which since its construction has not undergone major architectural changes, has reached our days as it was configured in its creation, adding the traces of the passage of time and interventions that have suffered polychromies. Because of the conservation situation, it was decided to have an interdisciplinary project for the structural study of the work, an exhaustive study of the materials and their state of conservation. The study of the materials includes the identification of stone supports, mortars, the pictorial technique of the original and added polychromies, and the superficial patinas. On-site studies were carried out by ground penetration radar (GPR) and X-ray fluorescence (XRF). Among the techniques used in laboratory were optical polarized light microscopy (MO-LP), X-ray diffraction (XRD), scanning electron microscopy with microanalysis (SEM-EDX) and Fourier-transform infrared spectroscopy (FTIR). The study allowed to determine the different pathologies of alteration and degradation of stone substrate and polychromies, chromatic alterations, biological patinas, etc. During this study, it was demonstrated that the diagnosis of wall paintings is a complex issue that needs to be addressed in a multidisciplinary approach, where scanning electron microscopy with microanalysis is the key methodology to get a deeper understanding of subsurface characterization of wall paintings and highlight the weathering processes. In a second phase of previous studies, this technique (SEM) has been used in assessing the viability of consolidation systems and cleaning both the stone and the polychrome.