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This paper explores the potential of software scaffolds, designed using activity theory, to support teachers in guiding students as they engage in inquiry around complex systems concepts. Early elementary students (aged six to seven) were randomly assigned to mixed-ability groups of five students (N=30) who participated either in a 30 minute activity consisting of either a scaffolded, teacher-led inquiry session with the BeeSign simulation software or a teacher-led book reading session, both of which centered on honeybees collecting nectar. Results indicate that students in the BeeSign condition learned more about honeybees from a complex systems perspective. Analyses explore how the teacher in the experimental condition was aided by the software scaffolds to help students engage with the complex systems concepts.