The study, which mixed qualitative and quantitative methodology, was conducted from June 2018 to February 2019 by involving at least 980 students and 168 lecturers of IRE Programme in Tarbiyah Faculty and 16 Focus Group Discussion (FGD)s with a total of 354 participants. The research was conducted in 18 Islamic higher education institutions and universities across 8 cities, namely Padang, Lampung, DKI Jakarta- Banten, Yogyakarta-Solo, Malang, Makassar, Banjarmasin, and Mataram. The results of the study indicate that the production system of prospective Islamic Religious Education teachers only has low resilience and is generally vulnerable to the spread intolerance and radicalism. There are at least six factors that contributed to this; first, the student recruitment process only takes into account potential student’s high school grade and hence hardly takes in students with the right characteristics that are needed to be a good IRE students. Students from pesantren or madrasa should have been prioritized, unfortunately this was not the case in most universities. Second, the philosophical foundation in which the programme lays itself is vague and unclear. Hence, most of the curriculum puts more emphasis on the pedagogical aspect, instead of the core knowledge on Islamic Religious Education. Third, students’ and lecturers’ understanding of Arabic language, as the main language of most textual sources in Islamic Education, is relatively low, and hence limit the sources from which students and lecturers can expand their knowledge. Fourth, there is lack of elements that encourage critical thinking among students neither in the curriculum nor syllabus. Fifth, students’ extracurricular activities are dominated by conservative groups. Lastly, religious moderation which has been an important value in Islamic universities has begun to erode to a direction that tends to be conservative, and even radical.