This study explored the relationship between instructional supervision of school heads and teachers’ perceptions of school climate in selected public secondary schools in Region XI, Philippines, using a convergent parallel mixed-methods design. The quantitative phase involved 400 teachers who completed a validated survey measuring instructional supervision concept and purpose, planning and preparation, organization and implementation, and dialogue and feedback and dimensions of school climate such as deviant behavior, school well-being, and subjective unsafety. Quantitative data were analyzed using descriptive statistics, Pearson correlation, and multiple regression, while qualitative data from semi-structured interviews with six teachers were thematically analyzed to explain and elaborate on the statistical findings. Results revealed that instructional supervision was rated high to very high, while school climate was rated moderate to high. A very weak but significant positive correlation (r = 0.080, p = 0.05) was found between instructional supervision and school climate. Regression analysis showed that concept and purpose and organization and implementation significantly influenced teachers’ perceptions of school climate. Qualitative findings highlighted three key themes: (1) supportive supervision builds trust, (2) professional growth opportunities, and (3) impact on school relationships. Overall, the study concludes that while instructional supervision contributes to a positive school climate, its influence is limited and context-dependent. Supervision practices that are mentoring-oriented, purposeful, and consistently implemented promote trust, collaboration, and professional growth. It is recommended that school heads strengthen developmental supervision and adopt trust-based leadership approaches aligned with SDG 4: Quality Education to enhance both teacher morale and the school environment.