Being a part of Religious Education Institution, named Pondok Pesantren, UNIDA Gontor adopt boarding system. This is typical of Pesantren system of education and therefore the students are under the guardian of the Head of Pesantren, usually called Kyai (religious leader). In this case, the guardian of UNIDA Gontor students are Dr. KH. Abdullah Syukri and KH. Hasan Abdullah Sahal, assisted by Deputy Rector of Student Affairs.
Like pesantren system of education, the campus of UNIDA Gontor has not only three but four education centers that consist of mosque as the center of activities; Kyai, a religious leader as central figure, boarding house as the representation of family and society, and academic activities as the representation of formal education or school. By those four centers of education students and teachers could live together under the shadow of Islamic values such as sincerity, simplicity, self-reliance, Islamic brotherhood and freedom. All these Islamic values and others dictate all daily activities in the campus of boarding house system.
The system is designed specially to form educational environment where students could interact with teachers to inculcate their knowledge and experiences directly. In addition, in the boarding system students have a Council to manage their own activities, for the development of their spiritual, intellectual and physical potentiality, including the enforcement rules and regulation of their own. In this boarding house campus with all its facilities, students could freely carry out their activities in all aspects according to their respective talent, under the guidance of tutors.
Since the academic and non academic activities are integrated in one system, the assessment of academic achievements of students is combined with that of non-academic achievements, so that the whole potentiality and achievement of the student in all field during their study at UNIDA Gontor could be identified. This is also to prevent the imbalance intellectual, spiritual and physical development of the student.