Treatment teams providing transgender-affirming medical care are inherently faced with various kinds of moral and ethical dilemmas and questions, which are becoming even more pressing due to increasing treatment numbers and public attention for transgender care. Little is known about what kinds of moral and ethical challenges manifest in clinical practice. The aim of the present research was to map the moral and ethical challenges of healthcare professionals working in a specialized multidisciplinary transgender care center. Over a period of 7 months, during a focused ethnographic study, data were collected through participant observation of multidisciplinary team meetings, observation of individual psychodiagnostic assessment sessions with clients, and analysis of transcripts and reports of a series of moral case deliberations. A thematic content analysis of the data identified various implicit and explicit moral and ethical challenges around the following six themes: (1) assessing eligibility; (2) content of treatment; (3) sequential order of the treatment steps; (4) role of the clinical guidelines; (5) differing notions regarding gender identity, and (6) decision-making process. Our research provides a detailed insight into the way healthcare professionals experience these moral and ethical challenges and how they are related to (local) guidelines, the multidisciplinary character of GD care, and its inherent implicit and explicit gender norms. Our findings suggest that good transgender care may profit from continuous multidisciplinary deliberation of and sensitivity toward the normative dimension of transgender care. The paper ends with recommendations for ethics support mechanisms in transgender care.