This paper diagnoses scientifically the physical and chemical deterioration of some Jordanian monumental buildings as a result of using wrong conservation techniques and improper treatment materials. According to the scientific guidelines and international charters, conservation and treatment works followed in two of the most important archaeological sites in Jordan (“Aglun citadel and Jerash City”) had been evaluated for assessing their validity and stability over the time. To achieve this objective, some of the scientific techniques and technical methods were followed such as evaluating the visual appearance changes by some special lenses, or magnifying glasses, and a Sony digital camera, defining some physical properties of ancient and modern samples of mortars and reinforced concrete through different scientific procedures; studying the micro-abrasion resistance of the samples by using Micro Tip I sand plasting instrument; defining the chemical and mineralogical composition by XRD technique, and studying the morphological features by SEM. Finally, the results proved that both sites are suffering severe forms of deterioration due to several factors and mechanisms such as increasing dampness of stone units and other building materials; surface crack patterns and pitting features; sulfation or salt-crustation and crystallization; breaking rocks surfaces down into smaller pieces, and corrosion of reinforcing steel bars.