Changes in the educational system need strong support from and connection to teachers who are a key factor in changing the chemistry classroom reality. Starting from the research, the importance of Beliefs and Pedagogical Content Knowledge (PCK) for teacher's actions in the classroom is well known. Both factors influence teachers' representation of science, their science knowledge and their organisation of knowledge. Thus, pre-service teachers' Beliefs and PCK need to be examined and sought out by educators. They should be developed into the direction of teaching chemistry due to recent reforms and teaching and learning theories. The presented longitudinal study evaluates Croatian pre-service Chemistry teachers' Beliefs about teaching and learning and their PCK about Particle Theory at the three different time points of their university teacher training programs. To determine their Beliefs participants were instructed to draw themselves as chemistry teachers in a typical classroom situation and to answer four open questions. Data analysis follows a pattern representing a range between the predominance of more traditional versus more modern teaching orientations in line with the educational theory focusing on the Beliefs about Classroom organisation, Beliefs about Teaching objectives and Epistemological Beliefs. The study on PCK is based on open-ended questions following the frame of PCK and Big Ideas about Particle Theory by Loughran et al. Data analysis follows the pattern of graduating the PCK of the participants at the novice, intermediate or advanced level. The data, regardless of the time point, depictured mostly traditional and teacher-centered beliefs about teaching and learning. The results about PCK show that pre-service chemistry teachers' PCK is mostly on the novice or intermediate level on the national level, regardless of the time point, while the results for particular universities show some differences. The level of the PCK depends rather on the component of the PCK than on the Big Idea. The conducted research provides not only an assessment of beliefs and PCK, but also their development through university education. Therefore, the study can be an excellent starting point for chemistry teacher education in university for detecting and developing Beliefs and PCK.