In this capacity, she transitioned with Dr. Töpfer to the Federal Ministry for the Environment, Nature Conservation and Nuclear Safety in 1987. She later headed up the division for international cooperation and the policy department. Cornelia Quennet-Thielen was the German delegate to the United Nations Framework Convention on Climate Change and the Kyoto protocol.
She then transferred to the Home Affairs Directorate-General at the Office of the Federal President in 2004 and later was named Deputy Director-General of the Department of Legal and Administrative Services. Cornelia Quennet-Thielen was named State Secretary and Director-General at the Federal Ministry of Education and Research (BMBF).