The Bundeswehr Institute of Microbiology along with the Technical University of Munich, the Ludwig-Maximilians-Universität (LMU) and the Helmholtz-Center constitute the Munich location of the German Center for Infections Research (DZIF).
The Institute runs the German Consulting Laboratory for Brucella since 2010 and the German Consulting Laboratories for plague and Tick-borne Encephalitis Virus (TBEV) since 2014 and 2015, resp.
Starting in 2010, the Institute is a member of the Center for Infections Research in Munich, a collaboration between institutions in Munich working in this area of research.
The Institute is the reference laboratory for Quality Control in Diagnostics (INSTAND) for Francisella, Coxiella and Anthrax.
The Institute has a collaboration agreement with the Institute of Microbiology, Immunology and Hygiene as well as the Institute of Virology of the Technical University of Munich since 2013.
Im Jahr 2016 wurde ein Kooperationsvertrag mit der Universität Stuttgart-Hohenheim abgeschlossen.