MARGISTAR uses Working Groups (WGs) to co-creatively move towards the solutions. This task force-based form of organisation is expected to be the most innovative and creative way of driving collaboration and knowledge co-creation.

Each WG is organised under a leader and vice leader. MARGISTAR's Management Committee (MC) is responsible for the Action's progress according to the project's established monitoring process. Additionally, a Core Group consisting of the Action Chair, Vice Chair, Short-Term Scientific Mission, and the leaders of the WGs ensures communication between the MC and the WGs. The Core Group prepares MC meetings, monitors the activities of the WGs, ensures that all milestones and deliverables follow the time schedule, and facilitates coordination and outreach among the WGs.