Moral character formation lies at the heart of Islamic education, yet sustaining it among adolescents facing constant behavioral and social pressures demands more than occasional moral instruction. Madrasah Tsanawiyah institutions are positioned to address this need through structured, ongoing habituation programs, and this study analyzes how such continuous habituation internalizes noble moral values at MTs Muhammadiyah 1 Ponorogo, identifies the resulting changes in student behavior, and examines the factors that support or hinder that process. Employing a qualitative case study design with a phenomenological perspective, data were gathered through observation, semi structured interviews with the headmaster, Islamic education teachers, and students, and documentation, then analyzed using the interactive model of data reduction, display, and conclusion drawing. Findings show that habituation practices including the 5S culture of smiling, greeting, and courteous conduct, congregational Duha prayer, Qur'anic recitation, memorization of daily prayers and hadith, and routines of discipline and responsibility measurably strengthened students' discipline, social concern, and habitual worship, driven primarily by teacher exemplarship, a religious school culture, program consistency, and family support, while uneven student awareness and external environmental influence constrained the process. These results position sustained habituation as a practical mechanism for character education that schools can replicate, extending the theoretical understanding of value internalization beyond isolated instructional moments toward institutionalized daily practice.