The conservation of monuments in Cairo represents a complex matter, influenced by the cultural context, the intrinsic features of a vast and heterogeneous architectural heritage, and the environmental conditions. Monument vulnerability levels strongly need to be systematized to delineate adequate programs of control, management, and intervention. Despite their leading role in the Egyptian architectural heritage, many monuments experience a critical state of conservation. Here, we report the results of a multi-scale investigation of the northern mausoleum in the complex of the Khanqah of Al-Nasir Faraj Ibn Barquq, located in the Islamic cemetery of Al-Qarafa Al-Kubra (Cairo, Egypt). Our research aims to increase the knowledge on the decorative stones used in the mausoleum and their decay processes. The investigation has been focused on the two areas of the building covered by a colored stone-slabs pattern: the floor and the qibla wall. A detailed architectural survey, carried out through photogrammetric techniques, provided a three-dimensional morphological knowledge of the mausoleum, upgrading the available surveys made about 50 years ago. The distribution of the materials has been verified by visual analysis, integrated by the first detailed mineralogical and petrographic characterization made on this mausoleum. The digital survey of the stone surfaces and the mineralogical, chemical, and petrographic analyses allowed a systematic mapping of the decay phenomena and some insights on the morphological alteration of single elements. The obtained results indicate a capillary rise of groundwaters and airborne pollution as the main degradation processes.