Since 2010, the Bundeswehr Institute of Microbiology together with the Technical University of Munich, the Ludwig Maximilian University and the Helmholtz Centre have formed the Munich partner site of the German Centre for Infection Research (DZIF).
The Institute has been operating the national reference laboratory for brucella since 2010 and for tick-borne encephalitis (TBE) since 2015.
The Centre for Infection Medicine Munich is an association of institutions at the Munich that focus on infectious diseases. Since 2010, the Bundeswehr Institute of Microbiology has been a member.
The Bundeswehr Institute of Microbiology is the reference laboratory for the INSTAND ring trials for Francisella, Coxiella and Anthrax diagnostics.
In 2013, an Agreement of Cooperation was signed with the Technical University of Munich. The collaboration partner is the Institute for Microbiology, Immunology and Hygiene and the Institute for Virology.
In 2021, an Agreement of Cooperation was signed with the Bavarian State Office for Health and Food Safety.