Schmalzried received the Wilhelm Jost Memorial Medal in 1994 and the Bunsen Medal in 2013. He is "External Scientific Member" of the Max Planck Institute for Biophysical Chemistry in Göttingen, member of the Göttingen Academy of Sciences, the Leopoldina, corresponding member of the Austrian Academy of Sciences and member of the Academia Europaea (1989). He was awarded an honorary doctor at the University of Stuttgart in 2003.