In this work, pilot cleaning interventions applied by a wet micro-blasting method on architectural surfaces of three historic buildings in marble and porous stone were evaluated in situ and in the laboratory. The investigation was performed on characteristic stone surfaces (marbles and porous stones) of the following historic buildings: Athens Academy and National Library of Greece in Athens center polluted urban environment and Bank of Greece in Piraeus marine environment. The materials of the facades were characterized, and the mechanism of decay was diagnosed. In addition, the cleaning method’s efficiency was evaluated based on the acceptability of the alteration of the cleaned architectural surfaces. Criteria were both aesthetic and physio-chemical. In particular, the architectural surfaces were examined in situ by the means of fiber optic microscopy, infrared thermography and colorimitry. In the laboratory, methods of investigation were optical microscopy, X-ray diffraction, scanning electron microscopy with energy dispersion by X-ray analysis, mercury intrusion porosimetry, Fourier transform infrared spectroscopy, conductivity and pH measurements. The majority of measurements and analyses were applied before and after the pilot cleaning interventions. Finally, the results of this study contribute to the development of an integrated methodology for the assessment of cleaning interventions applied on architectural surfaces.