GenomePT is coordinated by a Consortium Coordinator (CC), an Executive Board (EB) constituted by the coordinators of each node and a Project Manager (PM) responsible for financial matters, whose salary is supported by the University of Aveiro.

The EB is the decision making body of GenomePT. The CC implements the decisions made by the EB.

There is no fiscal autonomy, the PM is responsible for monitoring budget spending, writing financial reports and reporting to the CC, EB and FCT, each node is responsible for the management of its own funding and reporting to the PM.

The implementation team (IT) is responsable for the implementation of the Consortium Aggrement (workpackages and milestones).