This study investigates students’ conceptions of the carbon cycle with regard to the components they believe to be relevant to the carbon cycle, how they interrelate these components, the ways in which they trace carbon atoms, and the different levels of biological organisation they consider when doing so. A total of 142 students aged 13–16 years (grades 8–10) participated in the study. A total of 130 students completed the diagnostic task, and an additional 12 students completed both the diagnostic task and were interviewed. The primary results show that the students identified few components of the carbon cycle, tended to trace carbon atoms exclusively at the level of the organism, and had difficulties identifying organic carbon compounds, especially during processes in which carbon compounds are transformed. Considering the main educational implications, we recommend using an instructional strategy that traces carbon atoms across the different levels of biological organisation whilst connecting fragmented knowledge by integrating knowledge from physiology, biochemistry and ecology when teaching the carbon cycle.