In this study, Turkish prospective elementary science teachers’ understanding of photosynthesis and cellular respiration has been analysed within the contexts of ecosystem knowledge, organism knowledge and interconnection knowledge (IK). In the analysis, concept maps developed by 74 prospective teachers were used. The study was carried out with prospective teachers in their final year who were enrolled in the special teaching methods course. The results show that prospective teachers’ understanding of photosynthesis, cellular respiration, energy flow and matter cycling is quite different from one another’s. In addition, the present study revealed that prospective elementary science teachers showed weak understanding of energy flow and matter, cycling and cellular respiration concepts and IK category but they had strong understanding of photosynthesis concept. Prospective teachers also experience difficulties in understanding connections between macro- and microbiological systems. The study concludes with suggestions for more meaningful biology education.