In historical stone structures, material deterioration occurs over time due to climate-related reasons. In order to perform the correct interventions to these material deteriorations in the building, original material properties should be determined and restoration applications should be carried out in accordance with these properties. In this study, it was aimed to examine the material properties and problems of the Mor Yakup Church, in the Nusaybin District of Mardin Province, in order to create a laboratory guideline that reveals the material analysis to be used in the restorations to be made at the regional scale of Mardin. Although many studies have been carried out on the structure, up-to-date information and data on the chemical-physical decomposition processes that have occurred on the material over the years are lacking. In order to fill this gap and provide basic information for the proper preservation of the structure, the Mor Yakup Church was analyzed. This structure is important in that it is the first university of education in the world that has survived to the present day. In this study, field studies and laboratory studies were carried out to determine the textural, physical, chemical, mineralogical and mechanical properties of the material used in the building, and the changes it has undergone over the years. The weathering pattern, forms and profiles show that the limestone deteriorates due to the cement-containing mortars used in the building and environmental effects (especially from the exhaust gas effect). It has been determined that nitrate salt has a role in the intense black layering, which can be observed visually, especially on the stone surfaces.