Islamic religious colleges in Indonesia were created with a foundation of scientific integration between general science and religious science. This is one of the differences between public universities and religious universities in Indonesia. This research aims to analyze how the application of the concept of scientific integration in Islamic religious universities in Indonesia and how the opportunities and challenges posed by the integration of science. This research uses a qualitative approach with descriptive qualitative research. This research involves the managers of quality assurance institutions in Islamic religious colleges as informants of this research. Determination of research informants was done by purposive random sampling technique. Data were collected by interview and documentation techniques. The data collected is qualitative data which is analyzed by data triangulation technique. The results of the study indicate that one application of the concept of scientific integration at Islamic religious universities in Indonesia is the scientific paradigm contained in the composition of the educational curriculum used. The curriculum is structured with a different paradigm from public universities. In addition, the results of the study also show that there are opportunities and challenges obtained by the application of this scientific integration. for students, as well as making it easier to train and equip students' skills. Furthermore, the challenges obtained are obstacles to lecture management both from the aspects of students, lecturers, and the bureaucracy of study programs at the institution.