Professor Gottfried Otting was awarded the Wallmarkska Prize of the Royal Swedish Academy of Sciences in 1996.

Professor Gottfried Otting was awarded the FEBS Anniversary Prize of the Gesellschaft für Biologische Chemie in 1993.

FEBS Anniversary Prizes of the Gesellschaft für Biochemie und Molekularbiologie were initiated for the 10th anniversary of FEBS by generous capital gifts from Boehringer Mannheim GmbH and Eppendorf AG. They are awarded for outstanding achievements in the field of Biochemistry and Molecular Biology or related sciences. The awardees are selected from researchers under 40 years of age invited to give a lecture at one of the symposia or workshops held during a FEBS Congress and who are from within the FEBS area but not the Congress host country. The prize administration is managed by both FEBS and the Gesellschaft für Biochemie und Molekularbiologie (GBM), and up to two Anniversary Prizes of €2000 and a certificate are awarded each year.

Professor Gottfried Otting was awarded The ETH Zurich Latsis Prize in 1992.

The ETH Zurich Latsis Prize is awarded annually to young scientists from all fields. It focuses on excellent and independent research conducted at ETH Zurich. The prize was established in 1985 based on an endowment of the Fondation Latsis Internationale.

Professor Gottfried Otting was awarded the ETH Silver medal for PhD thesis.