There are many manuscripts in institutions that preserve and exhibit works such as museums, galleries, and libraries. These manuscripts are of great value because of their witnessing to the past and the historical and cultural significance they have accumulated. In addition to the organic nature and natural aging of the paper, which is generally used as the primary carrier material in these works, other materials used in the manuscripts are an obstacle to their preservation and reaching future generations. In this study, the animal encyclopedia consisting of 62 volumes, which was the first encyclopedia written on behalf of animals from the end of the 15th century to the beginning of the 16th century (1487–1501) of the Ottoman period, was examined archeometrically. A total of 40 samples consisting of paper, ink, dye and leather samples were analyzed using high performance liquid chromatography (HPLC-DAD) technique with diode array detector. After all, information on material characterization and deterioration product(s) was obtained. As a result of the analysis, vanillic acid, and its derivatives due to the natural aging of the paper and chrysophanic acid and its derivatives caused by fungi, which are the result of unfavorable environmental factors, were determined. It was concluded that the ink used in the manuscripts was iron-gall ink. In addition, it was determined that madder, weld, buckthorn, redwood, rhubarb or dock plants were used as dyestuffs. Also, it was determined that the leather samples were tanned with the vegetable tanning method using tannins. It is inevitable that this study will guide conservation experts in restoration and conservation studies.