Scanning microscopy techniques have emerged as powerful scientific tools for analysing materials of architectural or archaeological interest, since the commercialization of the first scanning electron microscopy instrumentation in the early 60s. This study is aimed at reviewing and highlighting the significance of several scanning microscopy techniques employed in the protection of built heritage. The diffusion of scanning electron microscopy with energy-dispersive X-ray spectroscopy analysis (SEM-EDX) is proven to be the widest among the available scanning microscopy techniques, while transmission electron microscopy (TEM) applications are steadily present in the field of built heritage protection. The building material characterization, the weathering mechanism investigation, and the development of compatible and performing conservation materials are some major research areas where the application of the aforementioned techniques is discussed. The range of techniques, along with aspects of instrumentation and sample preparation are, also, considered.