Background: Beginning teachers encounter several constraints with respect to scientific inquiry. Depending on their prior beliefs, knowledge and understanding, these constraints affect their teaching of inquiry. Purpose: To investigate quantitatively the longitudinal relationship between pre-service teachers' knowledge and attitudes on scientific inquiry teaching as part of a short teacher training. Sample: N = 121 pre-service teachers for teaching biology at the secondary level in Germany and Switzerland. Design and methods: We applied a pre-post-research design. As part of the teachers' attitudes we measured cognitive beliefs, affective states and self-efficacy. In addition, the teachers completed a test on content knowledge (CK) and pedagogical content knowledge (PCK). To examine the relationship between the different measurements, we applied structure equation modelling. Results: There was no significant relation between CK and PCK at both time points. The analysis further demonstrates that the PCK acquired after the training on teaching scientific inquiry predicts subsequent attitudes. Prior CK does not affect subsequent attitudes regarding teaching scientific inquiry. Moreover, prior attitudes do not substantially predict subsequent PCK and CK. In addition, prior teaching experience in biology explains individual differences, and self-efficacy attitudes predict changes in attitudes with respect to teaching scientific inquiry by the end of training. Conclusions: It appears that even short PCK training seminars may affect pre-service teacher attitudes towards scientific inquiry. Hence, teaching education programmes should be designed to broaden PCK.