Abstract Background The COVID-19 pandemic posed many unprecedented challenges to health care systems and public health efforts worldwide. Policy making and science were deeply intertwined, in particular with regard to the justification of health policy measures. In this context, ethical considerations were often 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. With this study, we therefore aim to explore the ethical challenges during COVID-19-related political decision-making in Switzerland as perceived by policy makers and scientists involved in policy making. We also explore the role ethics advice had during the pandemic response and what can be learned for future public health crises. Methods We conducted thirteen qualitative expert interviews with policy makers and scientists involved in decision-making on COVID-19 policy responses in Switzerland on the regional and national level. We used inductive content analysis to analyse the interviews. Results Among the multitude of ethical challenges highlighted, interviewees perceived making trade-offs between the common good vs. the individual good and between economic welfare vs. health of the population, as well as proportionality of the policy measures, and the capacity of the public to accept uncertainty as central. Interviewees had diverging opinions on whether ethical considerations were sufficiently raised and discussed on the Swiss policy level during the COVID-19 pandemic. Among the reasons why ethics was not sufficiently discussed, they mentioned a lack of time in the fast-paced dynamic of the pandemic, ethics as a complex subject area, the interconnectedness between ethics and law, too much focus on few topics (mostly on vaccination-related ethical questions), and power relationships, such as dominance of medical professionals over ethicists. They evaluated ethics support to have been adequately present in the decision-making process, but wished for 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 provides empirical insights into the ethical considerations of COVID-19 policy making in practice in Switzerland. It can help to develop ethics assistance for future crises and inform ethical health policy and decision-making not only in Switzerland, but also in other countries.