Plasters and mortars of the Church of the Annunciation (Tortorici, Sicily) were characterized, for the first time, both at the elemental and molecular levels, by means of portable X-ray fluorescence (XRF) and Raman spectroscopy, to achieve information on the “state of health” of the whole structure. The understanding of their degradation mechanisms and the identification of consequent degradation patterns can define the environmental factors responsible for interpreting the potential pathological forms that can impact the general building vulnerability. In this sense, the results obtained in this article provide relevant information to identify and address both the characterization of building materials and the fundamental causes of their deterioration. At the same time, if coupled with the attempt to supply a chronological order of the major restoration interventions carried out on the investigated site, they provide new insights to calibrate the models for building vulnerability studies.