The aim of this research was to evaluate and compare the efficiency of the flipped learning strategy with that of a conventional teaching method with respect to learning outcomes, cognitive gain, and perception and satisfaction with regard to the methodology used. The research was carried out during the 2021-2022 academic year and focused on a molecular biology course within a primary education Bachelor's degree programme, which included a total of 146 students. In order to assess the students' comprehension of the mechanisms involved in DNA replication, transcription, and translation, we employed two different methods: the multiple-select Central Dogma Concept Inventory (CDCI) and a concept-mapping activity. A three-point Likert-type scale questionnaire was used to investigate the pre-service teachers' perceptions of the methodological approach that we used. The results show that the flipped learning pedagogical approach not only increases pre-service teachers' performance but also enables them to develop higher level cognitive skills than with traditional methodology. However, several features of the central dogma processes remained poorly understood, probably because of the multilevel and invisible nature of the molecular biology, and the lack of knowledge of the molecular interactions that facilitate these processes. The pre-service teachers had a more positive perception of the teaching approach and their own competence when they followed the flipped model.