Abstract Background Policy making and science were deeply intertwined during the COVID-19 pandemic, particularly in justifying health policy measures with ethical considerations being at the core of decision-making trade-offs. However, not much is known about the actual ethical challenges encountered by policy makers and scientists involved in policy advice. This study aims to explore the ethical challenges in COVID-19-related political decision-making as perceived by Swiss policy makers and scientists involved in policy making, the role of ethics advice, and what can be learned for future public health crises. Methods Thirteen qualitative expert interviews were conducted with policy makers and scientists involved in COVID-19 policy decisions in Switzerland at regional and national levels. We used inductive thematic content analysis to analyse the interviews. Results Key ethical challenges included making trade-offs between common vs. individual good and economic welfare vs. health of the population, proportionality of policy measures, and public capacity to handle uncertainty. Opinions varied on the sufficiency of ethical considerations on the policy level. Constraints included a lack of time in the fast-paced dynamic of the pandemic, ethics as a complex subject area, its overlap with law, too much focus on few topics such as vaccination-related questions, and individual character traits, such as the dominance of medical professionals over ethicists. While ethics support was deemed adequately present in the decision-making process, there were calls for more ethics training, involvement of the public in the discourse, and for accompanying communication to build trust among the population for the future. Conclusions The study offers empirical insights into the ethical considerations of COVID-19 policy making in practice in Switzerland, providing a basis to enhance ethics support for future crises also in other countries. Key messages • This study uncovers the key ethical considerations in Swiss COVID-19 policy making, emphasizing constraints to sufficient ethical discussions. • Enhanced ethics training and greater public engagement is needed in future health crises to build trust and improve decision-making in future health crises.