Professor Baumeister’s main interest is the development of new tools and methods for the structural characterization of molecules and cells. He is particularly interested in the development of cryo-electron tomography for structural studies of molecular and supramolecular structures in situ, i. e. in their native cellular environment. A major focus of his work is the molecular machinery of protein degradation, in particular the proteasome, and autophagy.

He is a member of several academies including the Bavarian Academy of Sciences, the German Academy of Sciences, Leopoldina, the US National Academy of Sciences and the American Academy of Arts & Sciences.

He has received honorary degrees from the Masaryk University in Brno, Czech Republic and the Heinrich Heine University, Düsseldorf.