After compulsory military service, he studied biochemistry at the University of Tübingen, working for his final year at Dieter Oesterhelt's laboratory on ATPase activity of halobacteria.

Together with Michel and Huber, Deisenhofer determined the three-dimensional structure of a protein complex found in certain photosynthetic bacteria.

This membrane protein complex, called a photosynthetic reaction center, was known to play a crucial role in initiating a simple type of photosynthesis.

Their research increased the general understanding of the mechanisms of photosynthesis, revealed similarities between the photosynthetic processes of plants and bacteria and established a methodology for crystallising membrane proteins.

In 1986, he received the Gottfried Wilhelm Leibniz Prize of the Deutsche Forschungsgemeinschaft, which is the highest honour awarded in German research.