Background Pharmacists are increasingly involved in patient care. This new role in a complex healthcare system with demanding patients may lead to moral dilemmas. There has been little research into pharmacy ethics, and existing data are limited by their retrospective nature and small sample sizes. A thematic overview of the moral dilemmas experienced by community pharmacists is still missing. Objective To make a thematic overview of moral dilemmas experienced in daily pharmacy practice. Setting Dutch community pharmacy. Methods Dutch community pharmacists wrote a narrative about a moral dilemma they had experienced in clinical practice. The narratives were analysed using qualitative content analysis to identify underlying themes. Main outcome measure Themes of moral dilemmas. Results Twenty-two themes were identified in 128 narratives. These moral dilemmas arose predominantly during pharmacists' contact with patients and other health professionals. The relationship between the pharmacist, patient and other health professionals was complicated by other parties, such as legal representatives, health insurance companies, and regulators. Conclusion The moral dilemmas experienced by community pharmacists are more diverse than previously reported. The main dilemmas arose in their professional contacts, frequently when their professional autonomy was challenged by the behaviour of patients and other health professionals.