Inquiry is central in science education and therefore also in pre-service teacher (PST) education. In this systematic review of 142 empirical articles, we examine research on inquiry-based science education (IBSE) in teacher education between 2000 and 2022. The aim is to investigate how and with what outcomes IBSE is used in PST education. The included articles were categorised according to whether the PSTs worked with inquiry in the role of learner or in the role of teacher and also according to the cognitive domains of inquiry (epistemic, procedural, conceptual, social, pedagogical, or affective). The review shows that IBSE is used for PSTs to learn science concepts and processes and how to teach science through inquiry; however, few studies highlight the transition between these. In terms of cognitive domains, the procedural, conceptual, pedagogical, and affective domains dominated, whereas fewer articles addressed the epistemic or social domains. Favourable outcomes of IBSE for science understanding, teaching competence and improved attitudes or self-efficacy were reported. Challenges were noted, for example with implementing IBSE in school placement after having learned about it in campus-based courses. Finally, we offer recommendations for fruitful ways of implementing IBSE in PST education and suggest areas for future research.