The discourse on the integration of science and Islam is being realised through the establishment of various Islamic religious universities in Indonesia. One of the Islamic universities that accommodates this discourse is the Al-Qur’an Science University, Central Java, Indonesia (UNSIQ). This study aims to examine the basic concept of scientific integration at the UNSIQ and critically analyses the academic tradition and research development patterns based on the Lakatos research development pattern, both of which are hard-core and auxiliary hypotheses. This research shows that the scientific base at the UNSIQ has been structured in an awareness that supports the establishment of a distinctive academic tradition and scientific culture in the framework of al-Qur’an-based academic knowledge. However, research as auxiliary hypotheses in building scientific paradigm is still limited in certain disciplines and needs to be improved. This needs to be a common concern in order to increase the scientific base of the Syajarah al-Qur’an into a solid scientific paradigm.