Windesheim University, as it exists today, was established in 1986 through the merger of several educational providers.

This merger occurred gradually over several years.

It brought together the Academy for Journalism, the Academy for Social Studies from Kampen, and the School of Physical Exercise from Arnhem, to form the new institution.

Windesheim was administratively associated with VU University Amsterdam after the merger, but this arrangement ended in 2012.

In September 2006, Windesheim transitioned to the bachelor's/master's degree system.