Being able to make informed moral judgments in complex situations is considered a core element of professionals’ ethos. The didactical approach VaKE (Values and Knowledge Education) provides a possibility to address the development of the ability to make informed moral judgments. This study explores pre-service teachers’ (N = 81) mental representations underlying their moral judgment in the context of a VaKE (Values and Knowledge)-dilemma discussion using the example of a socio-scientific issue. The study aims to understand better how mental representations mediate moral judgments. The results of the cognitive-affective process system analysis indicate that moral judgments are based on a complex network of cognitions and affects elicited by different situational features such as specific factual knowledge. An important conclusion of this study is that the cognitive-affective process system analysis provides an effective method for analyzing mental representations in morally relevant decision situations. Moral judgments are highly situation-specific.