EJP SOIL operates on a strategic decision-making level and an operational level dealing with day-to-day coordination, technical, scientific and administration project management.

The strategic management's role is to align activities undertaken at the EU and national levels, particularly through review of Annual Work Plans. The operational management level is responsible for all project activities.  

The figure illustrates these two levels. The EJP SOIL consortium consists of strategic level programme managers as well as the operational level executive committee and day-to-day management support team. National hubs operate on the strategic level, whereas the European Commission and the Advisory board operates on both the strategic and the operational level. Finally, the Ethics board provides independent ethics assessment on to the operational level.