The Max Planck Institute for Terrestrial Microbiology was founded in 1991, with plans for three departments and one department-independent junior group. The founding director was Rudolf K. Thauer, Professor of Microbiology at the Philipps-Universität Marburg. In 1991, the first two departments were established – the Department of "Biochemistry" (headed by Rudolf K. Thauer) and the Department of "Biogeochemistry" (headed by Ralf Conrad). These two departments were initially accommodated in an interim-building and in rooms of the Faculty of Biology at the Philipps-Universität. At the same time, planning began for a new building to house the institute in the immediate vicinity of the Faculty of Biology.

The two departments moved into the new building on April 1, 1996. The Department of "Organismic Interactions" (headed by Regine Kahmann) was established in 2000. In 2004, the Department of "Biochemistry" was reduced to the size of a department-independent junior group, and in parallel the Department of "Ecophysiology" (headed by Lotte Søgaard-Andersen) was established. The Department of "Biochemistry" was closed in 2007, when Rudolf K. Thauer retired. Until the end of 2014, he was heading an Emeritus Group funded by the Max Planck Society. Victor Sourjik joined the institute in 2013 to establish the Department of "Systems and Synthetic Microbiology". This department is also part of the LOEWE Research Center for Synthetic Microbiology. The department is located in a university building next to the main MPIterMic building. In 2017 Ralf Conrad retired and the Department of "Biogeochemistry" was closed. In the same year the new Department of "Biochemistry and Synthetic Metobolism", headed by Tobias Erb (a former Max Planck Research Group leader), was established. When Regine Kahmann retired in 2020, Helge Bode began his directorship and since then is head of the Department of "Natural Products in Organismic Interactions" at the MPIterMic.

The MPIterMic have a strong tradition for successfully hosting department-independent research groups. In 1996 two department-independent research groups were established, one in "Symbiosis Research" headed by Barbara Reinhold-Hurek and one in "Ecophysiology" headed by Matthias Ullrich. B. Reinhold-Hurek accepted a professor position at the University of Bremen in 1999 and in 2002, M. Ullrich accepted a professor position at the International University Bremen. In 2007, Martin Thanbichler established a Max Planck Research Group (= the new name for a department-independent research group) in "Prokaryotic Cell Biology". In parallel, M. Thanbichler was also appointed to Junior Professor of Microbiology (tenure track) at the Philipps-Universität. M. Thanbichler was appointed full professor of Microbiology at the Philipps-Universität in 2014. In 2008, Sonja-Verena Albers established a Max Planck Research Group in "Molecular Biology of Archaea". She moved to the University of Freiburg in 2014 to take up a position as full professor of Microbiology. Lennart Randau joined the Institute in 2010 with his Max Planck Research Group "Prokaryotic Small RNA Biology" and moved to the Philipps-Universität Marburg, Department of Genetics, as Heisenberg Professor at the end of 2019. Eva Stukenbrock joined the institute in 2012 with her Max Planck Research Group on "Fungal Biodiversity" and moved to the University of Kiel and the Max Planck Institute for Evolutionary Biology in Plön as Max Planck Professor in 2014. Knut Drescher joined the institute in 2014 with his Max Planck Research Group on "Bacterial Biofilms". In 2015 he was also appointed to professor of Biophysics at the Faculty of Physics at the Philipps-Universität. Tobias Erb joined the institute in 2014 with his Max Planck Research Group on "Biochemistry and Synthetic Biology of Microbial Metabolism" until he was appointed director and head of the new Department of "Biochemistry and Synthetic Metabolism". Hannes Link joined the institute in 2015 with his DFG-funded Emmy Noether Research Group on "Dynamic Control of Metabolic Networks" and accepted a position as Professor of Bacterial Metabolomics at the University of Tübingen in 2020. 

In 2019, the institute was able to recruit Georg Hochberg as the new Max Planck Research Group Leader ("Evolutionary Biochemistry") and in 2020, three young junior research groups started their research: Katharina Höfer with her Max Planck Research Group "Bacterial Epitranscriptomics", Hendrike Niederholtmeyer with her Emmy-Noether Research Group "Cell-free Synthetic Biology", and Johannes Rebelein also with an Emmy-Noether Research Group "Microbial Metalloenzymes".

Wolfgang Buckel was a Max Planck Fellow at the institute from 2008-2017. Roland Lill was a Max Planck Fellow from 2009-2014. Martin Thanbichler was appointed to Max Planck Fellow in 2015. 

Campus Lahnberge before construction of the institute
MPIterMic under construction
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