In secondary science education, the learning and teaching of coherent conceptual understanding are often problematic. Context-based education has been proposed as a partial solution to this problem. This study aims to gain insight into the development of conceptual coherence and how context-embedded learning-teaching activities (LT) can promote this. We describe a case study in which a context-based lesson sequence about protein-rich food production was designed and conducted in a 10th-grade biology class. The conceptual framework consisted of transformations of forms of energy and matter in photosynthesis, cellular respiration, and biosynthesis. All relevant concepts and their interconnections (propositions) were captured in a reference concept map. A research scenario was used to evaluate whether the lesson sequence was conducted as intended. Learning outcomes were determined by analyzing written products on the occurrence of propositions from the reference concept map. Additional interviews provided insight into the development of conceptual coherence in relation to three context-embedded LT activities: using graphic visualizations, writing, and concept mapping. The results indicated that students improved in mentioning propositions from the reference concept map. Propositions relating metabolic processes and including forms of energy were still difficult. Finally, successful elements of the three LT activities are considered.