This study presents a comprehensive and systematic examination of a revered Qur an manuscript, commonly attributed to the third Islamic Caliph, Uthman b. Affan (d. 35/656), housed at the Topkapi Palace Museum in Istanbul, Türkiye (identified as H.S. 32). Halaseh offers a meticulous analysis of the manuscript's codicological, paleographic, and orthographic characteristics, explores its emendations, production date, and traces the manuscript's journey first to Cairo and then to Istanbul. Additionally, the study examines and categorizes its textual variants, including what are considered today as non-canonical and some that are not previously attested in the major qira at literature. This work not only sheds light on the transmission of the Qur anic text but also establishes a comprehensive framework for researching Qur an manuscripts. By integrating methods for examining these manuscripts as both physical artifacts and scriptural texts, Halaseh presents a holistic methodological approach to their scholarly study.