Background Whereas experience and cognitive maturity drives moral judgement development in most young adults, medical students show slowing, regression, or segmentation in moral development during their clinical years of training. The aim of this study was to explore the moral development of medical students during clinical training. Methods A cross-sectional sample of medical students from three clinical years of training were interviewed in groups or individually at an Australian medical school in 2018. Thematic analysis identified three themes which were then mapped against the stages and dimensions of Self-authorship Theory. Results Thirty five medical students from years 3–5 participated in 11 interviews and 6 focus groups. Students shared the impacts of their clinical experiences as they identified with their seniors and increasingly understood the clinical context. Their accounts revealed themes of early confusion followed by defensiveness characterised by desensitization and justification. As students approached graduation, some were planning how they would make moral choices in their future practice. These themes were mapped to the stages of self-authorship: External Formulas, Crossroads and Self-authorship. Conclusions Medical students recognise, reconcile and understand moral decisions within clinical settings to successfully reach or approach self-authorship. Curriculum and support during clinical training should match and support this progress.