Undergraduate biology majors require biological literacy about the critical and dynamic relationships between plants and ecosystems and the effect human-made processes have on these systems. To support students in understanding systems relationships, we redesigned an undergraduate botany course using an ecological framework and embedded systems modelling to support students in understanding the criticality of plant processes to the global carbon cycle. The class meetings included lectures, opportunities to develop systems models identifying the relationships between plant processes and other systems, reflections on their systems understanding and open-floor discussions about assigned primary and secondary readings that explored the relationships between plant systems, abiotic and biotic processes and global carbon cycling in their systems models. We used the systems models students developed at the beginning and end of the course to examine how their systems understanding grew. Our results suggest that at the beginning of term, students' ideas about plants were egocentric identifying the purpose of plants was to support human life and they did not consider relationships between plants and global carbon systems. By the end of the term, their models and reflections identified elements of a systems perspective and the students considered human impact on this delicate balance.