The Governing Committee is made up of the Minister responsible for the Environment of the Generalitat Valenciana or the person he/she delegates, the Minister responsible for Science or the person he/she delegates, the President of CSIC or the person he/she delegates, the Rector of the Universitat de València or the person he/she delegates, the Director and the Vice-Director of the Centre.

The Governing Committee shall be responsible for the superior management of the Center's activities, for informing and submitting to the competent bodies of the institutions participating in the Agreement the proposals that require their approval, and for approving the Center's ordinary budget project, and submitting it to the competent bodies of the institutions co-owning the CIDE.

The CIDE Board advises and reports to the Director on all matters affecting the operation of the Centre. It is made up of the director, who acts as chairman of the Board; the manager, who has no voting rights and acts as secretary; the vice-director; the heads of department and two staff representatives.

The Scientific Board is the forum for the deliberation of scientific matters at the CIDE. It is chaired by the Director and is made up of research staff belonging to bodies or scales of the CSIC, the University of Valencia and the Generalitat Valenciana, in which the degree of doctor is required for entry, and who hold positions at the CIDE. Likewise, members of the Scientific Staff are hired personnel with a doctoral degree who carry out their research work at the CIDE.

The direction of the CIDE is held since September 2018 by Dr. Patricio García-Fayos Poveda. A Vice-Directorate, the Management, the Departments and the Research Support Services depend on it.

The vice-directorate of the CIDE is held since February 2021 by Dr. Miguel Verdú del Campo.

The management of the CIDE is held, since April 2022, by Mr. Fernando Puig Algarra, who performs the administrative and management functions inherent to his position and on which the Administration, Secretariat and Maintenance depend.