The Ci2's organization is defined by its general regulation, which complies with the legal framework for Portuguese institutions dedicated to scientific research and technological development. Ci2 is part of the Polytechnic Institute of Tomar (IPT) and has autonomy over scientific activities. The Ci2 structure planned for 2025-2029 will consider the Universidade Autónoma de Lisboa (UAL) as a management institution.
The following coordination, management, and administrative bodies support the Ci2 activity:
The Scientific Council comprises the 947 integrated members and collaborators holding a doctoral degree.