The Governing Committee is composed of the Valencian minister in charge of Agriculture, Fisheries and Food of the Valencian government or the person delegated by the minister; the Valencian minister in charge of Science and Technology or the person delegated by the minister; the director of the CSIC or the person delegated by office of the Director, Vice-Director and General Manager.

It is in charge of the senior management of the centre, of informing and submitting to the competent bodies of the institutions participating in the Agreement the proposals requiring their approval, and of approving the proposed regular budget of the centre, and submit it to the competent bodies of the co-owning institutions.

The CIDE Board advises and reports to the Director on all matters affecting the operation of the Center. 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 two Department Heads and two staff representatives.

The Scientific Board is the forum for discussing the scientific issues of the CIDE. It is chaired by the Director and composed of the research staff belonging to researchers from the CSIC, the University of Valencia and the Generalitat Valenciana who hold a doctoral degree and work at the CIDE. The contracted staff who hold a doctoral degree and work at the CIDE are also part of the Scientific Board.

Since December 2024, Dr. Diego S. Intrigliolo Molina has been the interim and acting director of the CIDE. The Management, Departments and Research Support Services depend on him.

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.