Michel was born at Lüdwigsburg in Germany and educated at the University of Warburg, where he obtained his PhD in 1977. He moved to the Max Planck Institute for Biochemistry at Martinsried, near Munich, and remained there until 1987, when he moved to Frankfurt to head the biophysics division.

By 1970 chemists had succeeded in uncovering the basic chemistry of photosynthesis but little was known about the process at the molecular level. It was established that the process occurred in the photosynthetic reaction centers first identified by Roderick Clayton in the late 1960s. These are to be found embedded in the membranes of the photosynthetic vesicles. Within the reaction centers was a complex protein structure. Before further progress could be made, the structure of the proteins would have to be worked out, but first it would be necessary to crystallize the proteins.

Michel first tackled the problem in 1978. While it was relatively easy to crystallize water-soluble proteins, membrane proteins, which react with both fats and water, were only partially soluble in water. Michel used a molecule in which one end was attracted to water (hydrophilic) while the opposite end was water repellent (hydrophobic). By binding the hydrophobic ends of the organic molecules to the hydrophobic ends of the protein membranes the hydrophilic ends alone would lie exposed. The complex structure could then be dissolved in water and crystallized. By 1982 Michel had succeeded in crystallizing the membrane proteins of the bacterium Rhodopseudomonas viridis.

For this work Michel shared the 1988 Nobel Prize for chemistry with Johann Diesenhofer and Robert Huber.