In 2012 he was awarded the Accomplishment by a Senior Scientist Award by the International Society for Computational Biology.
von Heijne is a member of the Royal Swedish Academy of Sciences since 1997 and a member of the Nobel Committee for Chemistry from 2001 to 2009, and the Committees chairman from 2007 to 2009. In 2008, he received an honorary doctorate at Åbo Akademi.