The top organisational body is the Executive Board for the Centre, which consists of the Ci2A director, who chairs it, and the directors of the IC, CINC, IQOG and IQM.

This Board is in charge of reinforcing a rapid start-up of the scientific and technical services, as well as their constant update, so that they can provide excellent support to researchers from the four CSIC centres and Alcalá de Henares University.