In the present work the need to use cross-section analysis as a routine procedure to characterize physiochemical damage on building materials was evaluated using a combination of spectroscopic imaging techniques based on Raman spectroscopy, X-ray fluorescence spectroscopy (XRF), and scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM-EDX). First, samples for cross-section analysis required special preparation to avoid the loss of soluble and weakly anchored compounds and thereby ensure the representativeness of the analysis. To this end, samples were dry drilled and fractured with a single blow rather than cut to avoid friction. Cross-section analysis allowed surface deposition (crusts and patinas) to be differentiated from penetrating pollution and the affected depth to be determined. Elemental and molecular distributions were obtained to establish the origin of the compounds/elements found. Moreover, establishing the depth reached by the pollutant, which depends on the material porosity, can help to determine the physicochemical form of the pollutant. Finally, SEM-EDX images allowed surface and internal cracks, as well as the causes of these physical stresses, to be identified. As a result, surface analysis alone was shown to lead to incomplete or even incorrect conclusions that can be avoided by using cross-section analysis as a routine procedure when assessing the state of conservation of building materials.