School heads and teachers exert great effort to deliver quality instruction, yet academic challenges persist. To address bottlenecks in teaching and learning, intervention mechanisms rooted in evidence-based practices are implemented. Motivated by these concerns, the researcher examined the effectiveness of school-based intervention programs and innovative teaching strategies in public elementary schools in Laguna, and how these contribute to learners’ academic performance. The study aimed to determine the implementation of intervention programs, the extent of teachers’ use of innovative strategies, and the level of learners’ performance for School Year 2023–2024. A total of 300 randomly selected public elementary teachers from three school divisions participated, using multistage random sampling. Data were gathered through a researcher-made questionnaire and analyzed using correlational, qualitative, and descriptive methods. Findings showed that schools were implementing literacy and numeracy programs, and teachers used innovative strategies to a very high extent. Learners’ academic performance had a mean of 85.49, interpreted as “Very Satisfactory.” Results indicated a significant relationship between literacy-focused interventions—such as Project REACH and Project DEAR—and learners’ performance, while numeracy interventions showed no significant relationship. Innovative teaching strategies also showed no significant relationship with academic performance. The study recommends systematic planning for more effective literacy and numeracy interventions, continuous professional development for teachers, and adoption of a mastery approach for remediation. Engagement of the entire school community is encouraged. An Optimized Intervention Framework for Literacy and Numeracy Skills Enhancement is proposed, and future researchers are encouraged to conduct similar studies in other contexts.