This paper aims to characterize the different types of mortars used in a specific area most at risk of extinction at Apa Shenoute Monastery, including flooring, bedding, cladding and jointing mortars, in order to document their compositions and technologies. Due to the continuous exposure to erosion that has resulted in their deterioration over time, such a survey enables a proper understanding of their state of preservation, their composition as well as assists in the proper planning of future restoration work. To achieve this goal, representative samples of different types of applied mortars were subjected to in situ visual inspection, polarizing light microscope, X-ray diffraction, thermal analysis, grain size distribution analysis, and scanning electron microscope equipped with energy dispersive X-ray unit. Obtained results characterize optical, mineralogical, and technical properties of selected mortar samples. The results revealed the use of calcitic lime as a binder in all types of mortars with various Binder/Aggregate ratio, ranging from 1:1 to 2.3:1 with the exception of almost free aggregate mortars used in connecting mortars of clay pipes. Moreover, flooring and plastering mortars are composed of multiple layers. In the case of flooring mortars, it has been observed that fragments of limestone (0.5 to 3.5 mm) are added to the lower layer and fragments of brick dust are added to the upper layer as an artificial pozzolanic material. Different colours of the cladding and the jointing mortar of the kiln, varying between orange, grey-olive and black were attributed to the exposed firing temperature. The information gathered should be useful for specific selection criteria for compatible restoration materials and techniques.