The formation of black crust upon building stones and the resulting damage depend upon the fabric of the stone and atmospheric effects. The formation of black crust on limestone occurs more rapidly and distinctly compared to stones such as granite and sandstone, in which the mineral calcite is absent or in small quantities in its composition. In this study, black crust formation developed on the surfaces of limestone in İstanbul and Edirne, where important historical monuments belonging to the Byzantine and Ottoman Empires are located, were examined visually, microscopically, and experimentally. The factors causing the development of this crust and their effects on weathering were determined, and comparative analyses of the black crust with the sub-layer stone were made. In addition, by classifying the morphology, chemical structure, mineralogical composition, and damage to the stone by the black crust, chemical, and physical weathering that causes surface deterioration on the stone and back of the crust were examined. Physical (Schmidt hammer), mineralogical (X-ray diffraction), petrographic (polarizing microscopy), chemical (inductively coupled plasma-emission spectrometry, inductively coupled plasma-mass spectrometry, Fourier transform infrared spectrometry), and microstructural (field emission scanning electron microscopy with energy dispersive X-ray spectrometry) analyses were carried out to characterize this process. The black crust formation on limestone was shown to be caused by sulfation.