- Picoquant Young Investigator Award 2022 of the German Society for Biochemistry and Molecular Biology for Johannes Broichhagen
- ORCHEM Award for Young Scientists 2022 for Johannes Broichhagen
- Leibniz Start-Up Prize 2022 for ProSion (Joint spin-off of the Ronald Kühne lab from FMP and the Hans-Günther Schmalz lab from University of Cologne)
- Breakthrough of the Year 2020 of the Falling Walls Foundation in the category Life Science for Christian Hackenberger
- Feldberg Prize 2020 of the Feldberg Foundation for Volker Haucke
- Science Award 2018: Society needs Science of the Stifterverband for Thomas Jentsch
- Leonidas Zervas Award 2018 of the European Peptide Society for Christian Hackenberger
- Leibniz Start-Up Prize 2018 for Tubulis Technologies (Christian Hackenberger, Joint spin-off of FMP and Ludwig-Maximilians University Munich)
- Avanti Award in Lipids 2017 of the American Society for Biochemistry and Molecular Biology (ASBMB) for Volker Haucke
