This mixed-methods research study aimed to observe the changes in relational conceptual changes and achievement in photosynthesis and cellular respiration in 15 seventh-grade students using the variation theory of learning, a framework for contextual distinctions, and supports the Common Knowledge Construction Model (CKCM) for science education. The strategy used was prediction-observation-explanation, where students wrote and drew to express their macroscopic and sub-microscopic concepts, depicting any changes. Pre- and post-assessment tests were given to measure achievement in science. Through phenomenography analysis, five descriptive categories were generated for photosynthesis and nine for cellular respiration, revealing variations within and between students' ideas. Statistical tests showed significant improvements (p < 0.001) in photosynthesis and cellular respiration knowledge after implementing the CKCM learning sequence, with scores increasing from 37 to 77% and 33% to 72%, respectively. These findings suggest that inquiry-based learning based on relational conceptual change, guided by variation theory and an understanding of the nature of science, can lead to a deeper understanding of scientific explanations and improve overall science achievement.