This study aims to explore the mathematical proficiency, scientific reasoning, and metacognitive skills that contribute to the student’s academic performance in Physics. Data were gathered quantitatively by administering the Basic Skills Diagnostic Test, Lawson's Classroom Test of Scientific Reasoning, and Metacognitive Awareness Inventory to Grade 10 students in the selected high schools of District II of Ifugao Province from January to June 2023. Using the Raosoft calculator, 369 out of 405 students were randomly selected as participants. Relationships of the variables were analysed using Structural Equation Modelling (SEM) where the direct and indirect effect was shown. Based on the model, mathematics proficiency, scientific reasoning (Formal Operational, Late and Early Transitional reasoners), and metacognitive skills (declarative, debugging, and evaluation) had a direct effect on academic performance in Physics. The scientific reasoning skills – late transitional directly affect the metacognitive skills – procedural, conditional, planning, and information. Further, an indirect effect of mathematics proficiency on scientific reasoning and metacognitive skills, scientific reasoning to mathematics proficiency and metacognitive skills, and metacognitive skills on scientific reasoning and mathematics proficiency, toward academic performance was observed. Conclusively, a strong foundation in mathematical proficiency with the effective use of scientific reasoning and metacognitive skills were found to be key determinants of success in Physics. This suggests that educational institutions craft Physics curricula considering the development of students in mathematical proficiency, scientific reasoning skills, and metacognitive skills, while teachers develop activities that refine the direct and indirect effects of these variables to target a better academic performance in Physics.