This study aimed to construct an integrated Islamic Religious Education (PAI) and Science learning model at MI Muhammadiyah Sains Qur’an (MIM SAINSQU) Balong, Indonesia. A qualitative case study design was employed to explore existing integration practices and the institutional and pedagogical foundations underlying the development of the model. Participants were purposively selected and included the school principal, curriculum coordinator, PAI teachers, classroom or Science teachers, and selected students who were involved in or experienced the integrated learning process. Data were collected through semi-structured interviews, classroom observations, and analysis of curriculum and instructional documents. The data were analyzed thematically through familiarization, coding, categorization, theme development, and interpretation, followed by synthesis of the findings into the structure of the proposed model. The findings indicate that PAI–Science integration at MIM SAINSQU Balong is organized around Qur’an-oriented contextualization, scientific inquiry, Islamic values, environmental learning, active student participation, teacher facilitation, contextual learning resources, and cognitive-affective assessment. These findings informed the construction of an integrated PAI–Science learning model that organizes the relationship between Islamic values and scientific learning within the school’s specific educational context. The study’s qualitative contribution lies in translating existing institutional practices into a coherent, context-bound learning framework. The proposed model has not yet been tested for feasibility, validity, or effectiveness and therefore requires subsequent empirical validation and classroom trials.