All teacher trainers often ask ourselves about the effectiveness of the teacher training we implement.. Although many universities provide the scores of the opinion surveys on teaching answered by the students, this is an external indicator, and it is necessary to plan a more systematic evaluation to triangulate qualitative and quantitative results taking into account the objectives set. Furthermore, as the emotions experienced by the students are key in the teaching-learning process, in this study, we present an evaluation design that meets the above characteristics, as well as we show results obtained with a semi-open questionnaire about the emotions that pre-service Primary teachers declare feel in a Science Education course. This course has the special distinction of being focused on a Model-Based Inquiry framework, in which pre-service teachers make explicit and implicit reflections on: what science is, and how it works, why people need to learn science, how people learn science, and how to teach science. Moreover, they are actively engaged in a learning process by an Inquiry-Based Science Education approach that can be used as methodological model to teach.