Teachers' professional knowledge is considered one of the most important predictors of instructional quality. According to Shulman, such professional knowledge includes content, pedagogical content and pedagogical knowledge. Although recent research shed some light on the structure of the dimensions of professional knowledge, little is known how teacher education impacts pre-service physics teachers' professional knowledge. In an effort to address this issue, we examined the content, pedagogical content and pedagogical knowledge of N = 200 pre-service physics teachers enrolled in different years of teacher education at 12 major teacher education universities in Germany. We used structural equation modelling (1) to examine the relations amongst pre-service physics teachers' content, pedagogical content and pedagogical knowledge, (2) to explore how the three kinds of knowledge and their relations differ across different stages of teacher education and (3) to identify factors affecting the level of each component of professional knowledge. Our findings suggest that content, pedagogical content and pedagogical knowledge represent distinct types of knowledge. Furthermore, our findings show that in the first years of professional education, pedagogical content knowledge is more closely related with general pedagogical knowledge while in later years, it is more closely related with content knowledge, suggesting that it develops from a general knowledge about teaching and learning into knowledge about the teaching and learning of specific content. Finally, beyond school achievement and years of enrolment as predictors, we find in particular the amount of classroom observations to have a positive impact on the professional knowledge of pre-service physics teachers.