Contemporary instructional design has emphasized measurable achievement while giving limited attention to spiritual development. Although Islamic boarding schools (pesantren) have long cultivated character, spirituality, habituation, and character education are commonly studied as separate domains. This study proposes Systemic Spiritual Pedagogy as an integrated framework for spiritual character formation. Using a qualitative single-case study at Amanatul Ummah Islamic Boarding School, Indonesia, data were collected through participant observation, semi-structured interviews, and document analysis. The findings reveal three interconnected mechanisms: (1) institutional integration of spirituality into educational planning and regulations; (2) systematic habituation through twenty-four-hour religious, disciplinary, and social practices; and (3) continuous multidimensional evaluation of students’ academic, behavioral, disciplinary, and spiritual development. These mechanisms form a unified pedagogical cycle linking planning, implementation, and evaluation. By integrating Gagné’s Conditions of Learning with Al-Ghazali’s tazkiyatun nafs, the study extends instructional design theory and provides a systematic framework for embedding spirituality into holistic education.
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