ELIXIR-IT is coordinated by the JRU Manager assisted by the Executive Committee. The General Assembly is the highest body of the JRU and is composed by the JRU Manager, the Coordination Committee and the other delegates from the institutions part of the JRU.

The JRU has also a Technical Coordinator (TeC) and a Training Coordinator (TrC). Furthermore each institution appoints a Local Technical Coordinator (LTeC) for local organizational and coordination duties.