The Faculty of Science participates in the following interdisciplinary research institutes:
- A'dam Center Business Analytics (ACBA)
- Amsterdam Center World Food Studies (ACWFS)
- Amsterdam Institute for Molecules, Medicines and Systems (AIMMS)
- Amsterdam Public Health (APH)
- Amsterdam Movement Sciences (AMS)
- Amsterdam Neuroscience (AN)
- ARCNL
- Amsterdam Sustainability Institute (ASI)
- CLUE+
- LaserLaB
- Nationaal Instituut voor de Kernfysica en Hogere Energiefysica (Nikhef)
- Sarphati Amsterdam
- TALMA
- The Network Institute (NI)