Teaching responsible conduct of research (RCR) to PhD students is crucial for fostering responsible research practice. In this paper, we show how the use of Moral Case Deliberation—a case reflection method used in the Amsterdam UMC RCR PhD course—is particularity valuable to address three goals of RCR education: (1) making students aware of, and internalize, RCR principles and values, (2) supporting reflection on good conduct in personal daily practice, and (3) developing students’ dialogical attitude and skills so that they can deliberate on RCR issues when they arise. What makes this method relevant for RCR education is the focus on values and personal motivations, the structured reflection on real experiences and dilemmas and the cultivation of participants’ dialogical skills. During these structured conversations, students reflect on the personal motives that drive them to adhere to the principles of good science, thereby building connections between those principles and their personal values and motives. Moreover, by exploring personal questions and dilemmas related to RCR, they learn how to address these with colleagues and supervisors. The reflection on personal experiences with RCR issues and questions combined with the study of relevant normative frameworks, support students to act responsibly and to pursue RCR in their day-to-day research practice in spite of difficulties and external constraints.