This study evaluated the effectiveness of research-based instruction, specifically Problem-Based Learning (PBL) and Inquiry-Based Learning (IBL), in enhancing active learning engagement and scientific literacy among Grade 9 students in Mauban, Quezon. Motivated by persistent challenges in science education, the study investigated how these instructional approaches influenced students engagement in terms of interest, interaction, and active cognitive processing. A quasi-experimental design using cluster sampling was employed, involving 64 Grade 9 students from Manuel S. Enverga Memorial School of Arts and Trades. Data were gathered through pre- and post-assessments, formative assessments, a Likert-scale survey, and a criteria-based performance assessment. Paired and independent samples t-tests were used to analyze the data. Results indicated that both PBL and IBL positively influenced active learning engagement and improved scientific literacy, particularly in the domains of creativity and collaboration. While PBL demonstrated slightly higher engagement outcomes, it did not produce a statistically significant effect on critical thinking. No significant differences were observed between the post-assessment performances of the two instructional groups. These findings suggest that both PBL and IBL are effective in promoting active learning and developing key components of scientific literacy among secondary students. Future research should investigate the contextual factors that may impact the implementation and outcomes of research-based instructional strategies.