Previous research suggests that the use of metaphors in science education have both possibilities and challenges. In this study, we analyse the role of metaphors in meaning-making in the upper primary science classroom. We investigate the potential of metaphors about nutrient uptake occurring in classrooms in which an animation was used. To identify metaphors in the classroom interaction, we have applied an analysis according to systemic-functional grammar (SFG), rooted in social semiotic theory. The present study indicates that the use of metaphors can play an important role in scientific meaning-making, since, in that way, students and teachers can make meaning about scientific processes and functions before having access to the scientific terminology. However, if metaphors are to be functional tools for meaning-making in science education, the teacher has an important role to play in, among other things, explicitly connecting the metaphors and everyday language to scientific concepts. We argue that metaphors based on functional similarity have a high affordance for making meaning about complex processes, such as nutrient uptake.