Over 120 scientists work together in CoTeSys. In order to structure their work the organisation of CoTeSys is as follows:

The CoTeSys cluster is a research consortium and is organized according to the statutes signed by the host (speaker) university TUM and all participating institutions. Members of CoTeSys-II are the Principal Investigators (PIs) and, in addition, all independent Junior Research Group Leaders (iJRG leaders).

Members and associate members are eligible to propose projects for possible CoTeSys-II funding. The cluster is organized by the General Assembly (all members and associate members), the Extended Board (EB), the Executive Group (EG), the Cluster Coordinator, the Co-Coordinator, the General Manager (GM), the Research Area leaders, the Cross Area leaders, and the Scientific Advisory Board.