The COVID-19 pandemic is a complex, multifaceted and rapidly changing challenge. In times of crisis, when scientific evidence is limited, fragmented or even missing, the application of the concept of evidence-based policy making is challenged and advisors face difficult times when providing guidance for policy makers. We argue that these dilemmas can be tackled by transparency, trust and open communication. This is not only between advisors and policy makers but also with the general public as handling the pandemic is a socio-political challenge that goes beyond the mere concept of emergency preparedness and rather impacts all areas of life and civil society.