Although Higher-Order Thinking Skills (HOTS) are mandated by Indonesia's Merdeka Curriculum, their integration into Islamic Religious Education (IRE) remains poorly documented, particularly in pesantren-based schools where religious mastery has traditionally been prioritized over analytical reasoning. This study describes and analyzes how IRE teachers at a pesantren-based junior high school in Kediri City plan, implement, and evaluate HOTS-oriented instruction. Using a qualitative case study design, data were collected from IRE teachers, the school principal, and students through semi-structured interviews, classroom observation, and document review of lesson plans and assessment instruments, and analyzed using the interactive model of Miles, Huberman, and Saldaña. The findings show that teachers translate C4–C6 cognitive objectives into problem-based learning that requires students to analyze contextual moral issues, evaluate them against Islamic teachings, and propose faith-based solutions most distinctively, by consistently anchoring higher-order cognitive tasks in religious-normative reasoning rather than generic critical thinking. Assessment was realized through contextual essay items, case-based questions, and performance tasks (presentations, projects, portfolios) explicitly designed to elicit analysis, evaluation, and idea generation rather than recall. However, teachers continued to struggle with formulating valid HOTS test items and allocating sufficient instructional time. This study contributes an integrated, context-specific account of HOTS implementation that connects academic reasoning with the cultivation of Islamic values in pesantren-based education.