Although there is an increasing emphasis on the importance of systems thinking skills in science education, there is little reported on the empirical design process of adaptive and interactive visual learning environments for developing these skills in classroom settings. Therefore, the purpose of this study is to provide a theoretically and teacher-informed design process of a learning environment that supports the development of grade 7-9 learners’ systems thinking skills in the context of the carbon cycle. To respond to this aim we describe our iterative and theory-based design process by highlighting the main design activities and the rationale behind them, including: 1) content conceptualisation, 2) pedagogical (teacher) input, and 3) adaptive characteristics. The outcome of this process has resulted in an adaptive interactive visual learning environment with multiple learning tasks and quizzes organised in three modules. Each module is designed with coherent learning objectives aligned with a hierarchy of systems thinking skills and the Swedish school curriculum. Focusing on the carbon cycle, our work aims to provide a personalised learning experience for learners in grade 7-9 in scaffolding different levels of systems thinking.