CiiEM developed its 2025-2029 strategic plan by drawing on the Egas Moniz Strategic Plan, the institution's ISO 9001:2015 certification, the European Research Agenda, and CiiEM's mission, ambition statements, and values. The development process also incorporated data from a SWOT analysis and benchmarking, and involved CiiEM's community through iterative consultations.

The strategic plan is centered around five strategic objectives: fostering innovative research on a global scale, nurturing innovation and knowledge transfer, maximizing research quality and impact, engaging society through research, and educating and training leading minds.