At the time being, the undergraduate programs offered by UNIDA Gontor are eighteen departments of seven faculties which have been accredited by the National Accreditation Body of the Republic of Indonesia. The names of the department are:
| Faculty | Department | Available to |
| Faculty of Ushuluddin | Comparative Study of Religion | Male & Female |
| Aqeedah and Islamic Thought | Male & Female | |
| al-Quran and Tafsir | Male & Female | |
| Faculty of Islamic Education | Islamic Education | Male & Female |
| Arabic Language Teaching | Male & Female | |
| Faculty of Shari’ah | Comparative School of Jurisprudence and Law | Male & Female |
| The Law of Islamic Economics | Male & Female | |
| Islamic Finance | Male & Female | |
| Faculty of Economics and Management | Islamic Economics | Male & Female |
| Management | Male & Female | |
| Faculty of Humanities | International Relations | Male & Female |
| Communication Science | Male | |
| Faculty of Science and Technology | Informatics Engineering | Male & Female |
| Agro-technology | Male | |
| Technology of Agricultural Industry | Male | |
| Faculty of Health Science | Pharmacy | Female |
| Nutrition | Female | |
| Occupational Safety and Health | Male |
