This study examines multilevel factors shaping Indonesian student performances attending non-madrasah/sekolah and madrasah schools. Using multistratified sample design and grouped based on their school system, data from 30 schools, 64 teachers, and 1,319 students were analysed. Focusing on student, teacher, and school-level variables, hierarchical linear modelling revealed that reading difficulties and anxiety, along with school climates emphasizing achievement pressure and discipline, significantly influenced reading outcomes in both groups. Students grappling with heightened learning complexities and anxiety faced the greatest challenges. Interestingly, madrasah students thrived within competitive environments emphasizing high achievement pressure and minimal disciplinary constraints, while sekolah students who excelled in settings that valued discipline over relentless achievement pressure performed better. Unique influences emerged: peer relationships and anxiety directly affected reading scores in sekolah, while gender was the sole predictor in madrasah. Interaction effects among these multilevel factors in shaping student reading achievement across diverse educational settings were revealed.