Recent studies in science education have recognized a possible link between teachers’ beliefs about scientific knowledge and its practice in the classroom. Therefore, it is essential to promote the evolution of the pre-service teachers’ initial beliefs about methodologies for the teaching of chemistry in accordance with the discipline foundations and current recommendations on science teaching. We present the implementation and evaluation of a sequence of activities with a student-centred teaching approach for the training of pre-service science secondary education teachers. Inquiry, modelling, argumentation, as well as game-based learning are examples of the methodologies used. The results show a change of orientation from the epistemic beliefs prior to the programme implementation and highlight significant differences with respect to the relevance given by the teachers to carrying out research activities. For future teachers to develop professional competence, it is necessary to offer them opportunities to experience alternative methodologies during their training.