Background: The stage of the pandemic significantly affects people’s preferences for (the societal impacts of) COVID-19 policies. No discrete choice experiments were conducted when the COVID-19 pandemic was in a transition phase. Objectives: This is the first study to empirically investigate how citizens weigh the key societal impacts of pandemic policies when the COVID-19 pandemic transitions into an endemic. Methods: We performed two discrete choice experiments among 2181 Dutch adults that included six attributes: COVID-19 deaths, physical health problems, mental health problems, financial problems, surgery delays and the degree to which individual liberties are restricted. We used latent class choice models to identify heterogeneous preferences for the impacts of COVID-19 measures across different groups of respondents. Results: A large majority of the participants in this study was willing to accept deaths to avoid that citizens experience physical complaints, mental health issues, financial problems and the postponement of surgeries. The willingness to tolerate COVID-19 deaths to avoid these societal impacts differed substantially between participants. When participants were provided with information about the stringency of COVID-19 measures, they assigned relatively less value to preventing the postponement of non-urgent surgeries for 1–3 months across all classes. Conclusions: Having gone through a pandemic, most Dutch citizens clearly prefer pandemic policies that consider citizens’ financial situations, physical problems, mental health problems and individual liberties, alongside the effects on excess mortality and pressure on healthcare.