The present study investigates the relationship between multiple intelligences and the knowledge of content pedagogy among secondary teacher education students specializing in Natural Science. The framework of Howard Gardner’s Theory of Multiple Intelligences was adopted to assess the dominant intelligence profiles of the students and to explore how these intelligences correlate with their pedagogical knowledge in teaching science content effectively. The study employed a descriptive and correlational research design with a representative sample of secondary teacher trainees. Standardized tools were used to measure multiple intelligences and knowledge of content pedagogy. The findings revealed that students with higher levels of logical-mathematical and naturalistic intelligences demonstrated stronger pedagogical knowledge in Natural Science. Additionally, interpersonal and linguistic intelligences were also positively associated with effective instructional strategies. The study concludes that understanding learners’ multiple intelligences can significantly enhance teacher education programs by aligning pedagogical training with individual cognitive strengths. This integration supports the development of competent and innovative science teachers.