This paper aims to analyze and evaluate the function of two types of ancient mortars in the bathhouse at al-Muwaqqar archaeological site in Jordan to promote the awareness level of cultural heritage conservation of ancient buildings and mortars in Jordan. The conservation of archaeological structures requires a thorough characterization and identification of the mortar components before carrying out the restoration, after the preserved results, and during the restoration process to decide how it responds. This work creates an experimental contribution through FTIR to study the influence of organic components on the mechanical performance of the mortar. The application of new techniques in terms of sustainability and compatibility is nowadays more and more important to preserve historical monuments, especially in the context of the increasing damage to the mortar joints in the al-Muwaqqar site. The paper presents new results concerning the identification of the binding materials of mortars, especially the organic parts as egg white or other organic components used in the bathhouse to connect the mosaics, and the collection of further information for compatibility challenges. The results will provide a new pioneering approach application in Jordan in the field of ancient restoration using mortar. The study concludes that it is easy to identify all the organic components of the mortar using Fourier Transform Infrared spectroscopy (FTIR) in the different bands of the organic material supported by thermogravimetric analysis TGA/SEMEDX. The investigations of both methods have provided accurate information about the technology of mortar production and have indicated a proteinaceous additive in the mortar.