The development of the Bundeswehr Institute of Microbiology is closely linked to the history of the Bundeswehr Medical Academy in Munich. On 8 December 1959, the NBC Defence Medical Instruction and Working Group was set up as a component of the “Bundeswehr Medical School”, which was accommodated in the Prinz Luitpold Barracks in Munich. This group was not involved in research. It was responsible for teaching about the specialist field of NBC defence at the school.
On 1 November 1966, the Microbiology I and II departments were created as components of the NBC Defence Medical Instruction and Working Group. These departments comprised a total of 5 staff and were led by Colonel Dr. Ackermann (VC). This development enabled independent research on biological defence issues for the first time. Early experimental work took place in a provisional laboratory in the Prinz Luitpold Barracks. In 1973, the Studies and Science Department was set up at the academy. As part of its Study Group for Special Medicine and Natural Science, this department also included a Microbiology Section, which had the size of a laboratory group. In 1980, the Microbiology Section moved into new laboratories and premises at the Ernst von Bergmann Barracks, where the institute is still located today.
In 1984, the laboratory group became the Institute of Microbiology. The Institute's personnel grew to 25 staff, directed by Colonel Dr. Ahrens (VC). The Institute continued to belong to the Studies and Science Department of the Medical Academy. Experimental work was increased, and scientific cooperation with civilian research institutes commissioned by the Federal Ministry of Defence was expanded further.
In 1994, Colonel Ernst-Jürgen Finke, MD, was appointed Head of the Institute. In the same year, the first medical biodefence conference took place as a national conference with some international participation. In 1999, the Robert Koch Institute appointed one of the Institute’s laboratories as consultant laboratory for Tularaemia. In 2001, a biosafety level 3 laboratory was put into operation, creating the infrastructural conditions needed to work actively in the field of medical biodefence.
On 1 August 2002, the Bundeswehr Institute of Microbiology became an independent organisation comprising 65 staff. In 2006, it was evaluated by the Wissenschaftsrat – the German Council of Science and Humanities.
From 2008 until 2019, the Institute had been under the directorship of Colonel Professor Lothar Zöller. During this period, in compliance with the recommendations of the Wissenschaftsrat, third-party funded research has been expanded considerably. In 2010, the Institute was selected by the Federal Ministry of Education and Research as a partner institute of the Deutsches Zentrum für Infektionsforschung (German Centre for Infection Research). In the same year, one of its laboratories was appointed as consultant laboratory for Brucella. The Institute's capabilities in the field of biological reconnaissance were expanded considerably through the establishment of a newly developed and rapidly deployable biological laboratory with numerous fieldable diagnostic assays. Stationary bio-reconnaissance diagnostics were concentrated in a separate laboratory section referred to as the Central Diagnostic Unit and adapted to the provisions of a newly implemented quality management system. That way it was possible to have the entire diagnostic service spectrum accredited by the Deutsche Akkreditierungsstelle (DAkkS, national accreditation body for the Federal Republic of Germany) in accordance with the DIN EN ISO 15189 standard. In 2009, the traditional biodefence conference became the “Medical Biodefense Conference” and has since been held every two years as an international scientific congress. In 2014, one of the Institute’s specialised laboratories was appointed as consultant laboratory for plague and in 2015, another laboratory was appointed as consultant laboratory for tick-borne encephalitis.
Since 2010, the Bundeswehr Institute of Microbiology together with the Technische Universität München (TUM), the Ludwig-Maximilians-Universität München (LMU) and the Helmholtz Zentrum München have represented the Munich partner site of the German Centre for Infection Research (DZIF). In February 2013, a cooperation agreement was signed with TUM for close future cooperation between the Bundeswehr Institute of Microbiology and the university's Institute of Medical Microbiology, Immunology and Hygiene and the Institute of Virology. In 2016, the Institute concluded a cooperation agreement with the University of Hohenheim.
In 2019 Colonel Roman Wölfel, MD, PhD, DTMH was appointed Director of the Institute. He had previously worked from 2003 until 2016 in various departments of the institute.