This study analyzes the transformation and innovation of learning al-ḥifẓu wa khaṭṭī Al-Qur’an through digital integration at Al-Aqobah and Sakal Calligraphy Islamic boarding schools in Jombang, using a mixed-method approach to reveal how technology enhances learning quality and students’ readiness to face global challenges. The findings show that, first, the administrators of both pesantren hold a positive, inclusive, and transformative paradigm for applying digital technology in Qur’anic memorization and calligraphy-based learning. Second, the pesantren implement digital transformation by adopting and integrating technology across various aspects of learning, with stages adjusted to each pesantren’s takhassus (specialization). Al-Aqobah focuses on strengthening al-ḥifẓ Al-Qur’an supported by research and language competencies, while the Calligraphy Pesantren emphasizes the development of khaṭṭī Al-Qur’an and zukhrufah (ornamental design) through digital media. This digital transformation has also encouraged the emergence of various learning innovations in Qur’anic memorization and calligraphy instruction. A descriptive survey showed that 77.60% of respondents expressed positive perceptions regarding the implementation of digital transformation and learning innovation, while 22.40% considered its implementation less optimal due to limitations in technological infrastructure and digital competencies. In addition, 85% of respondents perceived that digital-based learning contributed positively to improvements in students' academic and non-academic achievements, indicating a positive trend in learning quality rather than statistical significance. These findings suggest that digital integration can support learning innovation while preserving the educational values and traditions of pesantren.