Religious education in madrasahs plays a vital role in fostering students’ character, spiritual awareness, and moral behavior. One of the strategies implemented to strengthen religious values is the habituation of Al-Qur’an literacy activities before classroom learning. This study aims to analyze the process of internalizing religious values through Al-Qur’an literacy at Madrasah Tsanawiyah An-Nur Atari Jaya. This research employed a qualitative case study approach. Data were collected through observations, semi-structured interviews, and documentation involving the head of the madrasah, Islamic Education teachers, homeroom teachers, and students. Data were analyzed using the interactive model of Miles, Huberman, and Saldaña, consisting of data condensation, data display, and conclusion drawing. The findings reveal that Al-Qur’an literacy functions not only to improve students’ Qur’anic reading competence but also to cultivate religious awareness, discipline, responsibility, and respectful behavior through continuous habituation. The internalization process occurred through the stages of value transformation, value transaction, and trans internalization. The trans internalization stage was reflected in students’ consistent participation in Qur’anic literacy activities, increased self-discipline, stronger responsibility in carrying out religious routines, and more respectful attitudes toward teachers and peers. This study concludes that Al-Qur’an literacy serves as an effective strategy for strengthening religious character education through continuous habituation, supported by a positive religious school culture.