Energy transfer in ecosystems is an abstract and challenging topic for learners. Metaphors are widely used in scientific and educational discourse to communicate ideas about abstract phenomena. However, although considered valuable teaching tools, metaphors are ambiguous and can be misleading when used in educational contexts. Educational researchers have found metaphorical patterns in scientific and everyday language that have been analyzed on the level of conceptual metaphors. However, little is known about the way students deal with crucial metaphors of specific science content. Using metaphor theory as a framework, the study presented here focuses on metaphors describing energy transfer through an ecosystem: "energy flow," "energy flow is not a cycle," "energy flow is a one-way street," and "energy loss." Applying qualitative content analysis, the usage of the metaphors was analyzed in 13 biology textbooks and 50 students' texts. We found notable differences between textbooks' and students' application of metaphors. Students often do not adopt the metaphors or use them as intended. For example, energy flow is a conventionalized metaphor for energy transfer processes, but students tend to use this metaphor in terms of a substance instead of a process. Implications for the use of these metaphors in biology instruction are derived.