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Purpose The COVID-19 pandemic and consequent strain on healthcare globally shed light on the concept of moral distress among healthcare workers, albeit to a smaller extent among doctors at emergency departments. This study aimed to examine moral distress as perceived by medical doctors working at emergency departments in Stockholm during the pandemic, with the purpose of investigating causes of moral distress and methods to manage moral distress. Methods Semi-structured interviews were conducted with twelve doctors working at two emergency departments. A questionnaire was developed based on previous research and the interviews were analysed qualitatively through thematic analysis. Results The themes ”The factors that precipitated moral distress”, “Experience of workplace support” and “Coping strategies” as well as seven subthemes and 15 codes were identified. The informants reported on various situations with different causes of moral distress. Common causes were resource depletion, such as hospital bed shortages, and following stricter triage criteria. Informants reported varying ways of managing moral distress. Conclusions Informants experienced moral distress when faced with challenges such as resource depletion, rules and regulations, and colleagues’ decisions. The informants who chose to seek support received it from their workplace, which helped them cope with their experiences. Some informants chose to not seek support.