Europa-Universität Flensburg hosts several institutes and centers that focus on interdisciplinary research and education. Key centers and institutes include:

1. ICES (Interdisciplinary Centre for European Studies): This center promotes research on European integration across disciplines such as social sciences and humanities. It supports research funding, networking, and the promotion of early-stage researchers, with a focus on sustainable conflict resolution through its affiliated Wasatia Graduate School for Peace and Conflict Resolution.

2. Center for Research on Sustainability and Transformation (CREST): Dedicated to addressing global challenges such as climate change, biodiversity loss, and social inequality, CREST serves as a hub for sustainability-oriented research.

3. Other Associated Centers:

   • KURS: Focuses on small and regional languages.
   • CaNoFF: Supports research on French studies and francophone regions.
   • Centre for Irish Studies: Explores Irish culture, literature, and history​

These centers facilitate collaborative research, academic exchange, and career development for researchers and students.