AEGIS operates within the framework of the ECPGR using the institutional machinery developed by ECPGR:
- The ECPGR Steering Committee has overall responsibility and oversight over the operation of AEGIS;
- The ECPGR Executive Committee has primarily a strategic oversight over the establishment and operation of AEGIS; as of March 2014, it has taken up the role previously assigned to the AEGIS Advisory Committee.
- The ECPGR Working Groups provide technical support, including through the preparation and coordination of Crop Conservation Work Plans and recommendations regarding proposed European Accessions;
- The ECPGR Documentation and Information Working Group provides information infrastructure, including reporting services through EURISCO and the National Inventory System;
- ECPGR National Coordinators also act as coordinators for AEGIS within their own countries, and serve as focal points for interactions with the ECPGR Crop Networks and Working Groups. They also serve as the link with Associate Members in their own countries, promoting and coordinating the designation of European Accessions and the development and management of the European Collection as a whole; and
- The ECPGR Secretariat provides support and coordination.