This study examines the implementation of deep learning within a holistic education framework to strengthen Islamic character through a transformative spiritual model in elementary education. The research analyzes the integration of Intellectual Quotient (IQ) and Spiritual Quotient (SQ) grounded in mindful, meaningful, and joyful learning. Employing a qualitative, holistic single-case study at SD Muhammadiyah Bantul Kota, Yogyakarta, data were gathered through participatory observations, documentation analysis, and in-depth interviews with the principal, teachers, and sixth-grade students. Data were analyzed using an interactive model involving condensation, display, and source triangulation. The findings reveal that deep learning effectively integrates cognitive and spiritual dimensions; for instance, science lessons transcend conceptual understanding by incorporating spiritual reflections on divine greatness. The three foundations of deep learning foster intrinsic religiosity, transforming practices such as prayer and dhikr into internal spiritual needs rather than mere formal obligations. Furthermore, the study identifies the emergence of a transformative spiritual culture evidenced by spontaneous Islamic behaviors, including honesty, empathy, and the "7S" values (Senyum, Sapa, Salam, Sopan, Santun, Syukur, dan Sabar (Smile, Salutation, Socialize, Soft spokenness, Stability, Shukr 'Gratitude', and Steadfastness). These results indicate that synthesizing deep learning with holistic Islamic education promotes balanced cognitive, emotional, and spiritual development, ultimately enhancing students' moral resilience and character formation in contemporary elementary education