This paper reports on the design of an innovative Electrochemistry course, part of a Chemical Science Engineering programme. Teachers have observed that their students' understanding of electrochemical concepts and phenomena is insufficient to attempt connections to further concepts, and to generate new knowledge in scientific problem-solving. A new course was required aiming to contribute to students' building mastery of concepts and deep insight into phenomena, both in and beyond the learning context. The course was designed tapping on ideas of inquiry-based learning and involving of conceptual modelling as a scaffold to learning. This pedagogical intervention departs from the consideration that conceptual modelling is an essential reasoning ability of (engineering) scientists and, consistently, it constitutes a key learning objective. Concurrent with the implementation of this course, an accompanying empirical investigation was set up to grasp how students learn electrochemistry with this novel pedagogical approach, and whether (and to what extent) there is any observable effect on the learning and transfer of electrochemical concepts. Both the instructional design of the course and the educational research design integrate considerations from Chemical Science, Philosophy of Science in Practice, and Education Sciences. The implications for engineering education and for educational research are discussed.