After a reorganisation, the Institute for Consumer Health Protection and Veterinary Medicine (BgVV) was established as the successor to the Federal Health Office.

The BSE crisis in 2000 caused extensive public discussion of consumer health protection, which ultimately resulted in a reorganisation. The objectives were a strengthening of consumer protection and better coordination of food safety between federal government, federal states and the European Union. The basis for the new organisation was an official report by Hedda von Wedel, the president of the Federal Audit Office at the time, which she had written in her capacity as Commissioner for Administrative Efficiency.

In order to improve transparency of government actions, risks concerning consumer health protection were to be evaluated and managed by different institutions. With the new organisation, the Federal Office of Consumer Protection and Food Safety, still a federal institute at that time, was created in 2002 as the authority for risk management. At the same time, the Federal Institute for Risk Assessment was created, which assessed risks independently of political influence and advised the federal government.

To set up the new BVL, twenty five employees started working in Bonn in May 2002. In addition, as part of the establishment of the federal office, the Plant Protection Product department came from the Biological Federal Institute for Agriculture and Forestry and the Feed department from the Federal Institute for Agriculture and Food. The specialist unit for the approval of veterinary drugs, which was integrated into the BVL along with a series of specialist food safety tasks, came, as part of the reorganisation, from the Federal Institute for Consumer Health Protection and Veterinary Medicine, which was absorbed into the BVL, the Federal Institute for Risk Assessment and the Federal Research Institute for Animal Health. In 2004, the BVL took over the approval of genetically modified organisms from the Robert-Koch-Institut. From December 2006 to May 2014, the BVL also took on tasks related to cross-border, collective economic consumer protection and the implementation of the Services Directive.

In May 2002, Dr Christian Grugel took over the management of the authority founded as the Federal Agency of Consumer Protection and Food Safety and was named president in mid 2003. Under his direction, the set up of the BVL took place to become a modern management authority. At the end of 2007, Dr Christian Grugel moved to the Federal Ministry for Food, Agriculture and Consumer Protection in order to head the consumer policy department. Dr. Helmut Tschiersky headed the BVL from 2008 to November 2019. Under Dr. Tschiersky's leadership, BVL underwent major changes. The office took on numerous new specialist tasks - for example in the areas of food fraud and food crime. Since December 1, 2019, Mr. Friedel Cramer has headed the BVL.