STEM teacher shortage remains a serious problem in secondary education in many European countries, despite many interventions and many research studies over the last decades. The observation that past interventions and research outcomes have not significantly contributed to reduce teacher shortage implies that places to effectively intervene in the teacher education system have not been found yet. In this article, a systems thinking approach is presented to evaluate the fundamental and structural problems of an academic teacher education system regarding STEM student entry. A thorough understanding of the systemic structure of a teacher education system is essential to identify leverage points for STEM teacher recruitment. Based on systems thinking principles and theoretical frameworks, a stepwise research framework was defined, which was tested in the Dutch academic teacher education system. First, potential factors of concern were identified based on the collection of many data such as existing public information, reports and long-term student entry data. These potential factors of concern were subsequently investigated by student surveys and structured interviews with stakeholders from science faculties and teacher training institutes. Synthesis of the results led to the identification of three leverage points for increasing STEM student entry in teacher training, which were all found at the organizational and structural level of the academic teacher education system. The systems thinking research framework presented in this article provides a valuable framework to address persistent problems in education and enables the identification of novel and potentially more effective interventions.