Science teachers should be able to notice student preconceptions in order to adapt instructions to their students' needs and support the learning process. Noticing as a core practice of teaching should thus be implemented early in science teacher education. A crucial prerequisite for noticing is knowledge about students' preconceptions, which is an important element of science teachers' pedagogical content knowledge. To enhance pre-service teachers' pedagogical content knowledge, flipped classroom approaches seem especially promising as they combine a theoretical introduction to important didactic concepts with a direct application of these concepts in profession-oriented learning tasks. Furthermore, flipped classrooms seem to satisfy the three basic personal needs of experience in competence, social relatedness, and autonomy according to the self-determination theory of motivation, thus enhancing learning. This intervention study investigates the effect of a course on physics didactics designed according to the flipped classroom approach on pre-service teachers' (N = 87) learning to notice student preconceptions. Specifically, we analyzed how pre-service teachers' perception of competence, social relatedness, and autonomy during course participation related to their noticing abilities. We found a significant increase (d = 0.40) in PSTs' noticing abilities, operationalized as absolute number of recognized preconceptions between pre- and posttest. However, this increase was not mediated by PSTs' perception of competence, social relatedness, and autonomy.