The IPB started life as the East German Institute for Biochemistry of Plants, which was a member of the German Democratic Republic’s Academy of Sciences. Kurt Mothes founded this institute in 1958, the first of its kind in Germany. Both he and his successor had strong backgrounds in the biological, pharmaceutical, and chemical sciences, which greatly influenced the research conducted by the institute.
In January 1992 the IPB was refounded to carry on the successful work of more than 30 years of research. Since then, the institute's buildings have been thoroughly modernised, and many new facilities have been added.
The IPB maintains a close connection with the nearby Martin Luther University Halle Wittenberg. Professorships and directorships at both institutions are jointly decided, and this close working relationship benefits both research and teaching.