This is a preprint of a book chapter which has been submitted to the upcoming edition of the Routledge Handbook of Empirical Bioethics. This version has not yet been peer reviewed or edited for consistency with other chapters. In this chapter we focus specifically on the methodological challenge encountered in deriving moral experiences—in this case moral challenges—within qualitative datasets such as transcripts of semi-structured interviews and focus groups. Drawing on a case study in gender-affirming medical care, we describe the interpretive and reflexive strategies we employed to describe healthcare professionals’ moral challenges from our qualitative data. Rather than offering a one-size-fits-all solution, we aim to provide practical insights and methodological transparency that may support other empirical ethics researchers in noticing inherent complexities and choosing ways of handling them. Ultimately, our goal is to contribute to the transparency and accountability of empirical research methodology in empirical ethics, and to help strengthen the professionalism and overall quality of the field of empirical ethics.