Since December 2014, De Jong has been heading the IHEF division of the institute and as such has been a member of the IoP directorate. He succeeds Daniel Bonn, who served as IoP director since October 2012. Bonn stays on in the directorate as head of the WZI division; Jan de Boer remains head of ITFA.

Paul de Jong is affiliated to the UvA since 2009, first as professor by special appointment with his main affiliation with Nikhef, the Dutch national institute for subatomic physics, and since 2012 as full professor. As a researcher he is a member of the ATLAS experiment at the Large Hardon Collider of CERN, which played a key role in 2012 in the discovery of the Higgs boson. Within the UvA, Paul de Jong is associated with the UvA research priority area GRAPPA.