Since the collections were owned from the first by the government of Styria, the Joanneum was for a long time in the hands of the state administration.
In 2003, after thorough consideration, it was transformed in a not-for-profit limited company called Universalmuseum Joanneum GmbH, to maintain competitiveness within the international museum industry.
In 2009, the Joanneum was given a new corporate design. In order to anchor the diversity of the collections in the name as well, the name of the former department of the Styrian Provincial Administration was also renewed: the Landesmuseum became the Universalmuseum Joanneum.
As of 2023, Marko Mele, PhD, and Josef Schrammel, MA, are directing Universalmuseum Joanneum GmbH.
To promote the global network of the company and especially to ensure a high-quality exhibition programme at the Kunsthaus Graz, partnerships with national and international museums and cultural institutions are proactively sought. The exhibition policy is to present all aspects of the permanent collections in a contemporary manner attractive to the public. A principal focus of attention is therefore to ensure that the various locations of the Museum work together as effectively as possible, and in doing so underline the unique character of the Universal Museum in all its diversity.
With the establishment of the Joanneum as a not-for-profit limited company, the Universal Museum has gained a greater degree of responsibility and autonomy in matters of staffing and budget. Nonetheless, the federal state of Styria is still the owner of the property and other assets in the Museum, just as intended by its founder Archduke Johann.