Coping ethically with dramatic changes such as those occurring in times of pandemics is a difficult challenge for animal facilities and for researchers using animals for scientific purposes. Managing such situations is impossible without a specific contingency plan. However, because pandemics are rare events, they have not been included in some disaster plans. We present here various ways to manage the broad and rapid changes that may be necessary during a pandemic, focusing on actions for optimizing the conservation of animals while ensuring continuous high standards of animal welfare. The proposed approach is graduated and encompasses research, researchers, animal caretakers, supply chains, and logistics.