CITI is managed by the Executive Board, led by the Director (Scientific Coordinator) and two vice-directors, elected by the Scientific Commission. The current CITI Director is Luis Caires, and vice-directors Nuno Correia, and Nuno Preguiça.

To promote agility, researchers are organized in agile, lightweight, goal-directed "team-projects", that may cut across thematic areas, giving rise to an effective "matrix" organizational model. Each team-project focus on a set of goals shared by all of its members, is led by a principal investigator, and subject to competitive use of plurianual funding.

Scientific activities are overseen by the Scientific Board, which includes all CITI researchers holding a Ph.D. degree. The Steering Committee is composed by the executive Board, Research Group Coordinators and two effective members elected by the Scientific Commission. The Advisory Board is composed by internationally recognized senior researchers, and nominated by the Steering Committee. Administrative support is provided by the host department, and specialized S&T management support by a STM grant holder.