The IISH has approximately 100 employees. In addition, a number of fellows and volunteers are working at the institute. 

The IISH is one of the 16 Institutes of the Royal Academy of Arts an Sciences (KNAW), which is financed by the Dutch Ministry of Education, Culture and Sciences.
The collections that have been submitted to the IISH are owned by or trusted to an independent foundation, the IISH Foundation. 
In 2016, the IISH joined forces with the Huygens Institute for the History of the Netherlands (Huygens ING) and the Meertens Institute to form the KNAW Humanities Cluster (KNAW HuC). 
The IISH has a board of directors with four members.