In the new millennium, the GSU continued on its chosen path towards achieving an educational profile in research and pedagogy. As early as 1999, in the wake of the structure and development plan, its specific status as a sports university was emphasised. The European higher education policy changed the academic landscape: The "Diplom-Sportwissenschaftler/in" degree had become a redundant model and was replaced by a Bachelor and Master degree program. Thus, new challenges were created, which required re-orientation in teaching and administrative structures.

In 2001, the GSU was to become a "European Sport University". A new education policy was the introduction of tuition fees with effect from the winter semester of 2006/07, which were abolished again in 2011, and the introduction of the Freedom of Higher Education Act in 2007, in which it was laid down that the universities, inter alia, were granted far-reaching autonomy with respect to the financial sector.

In 2006, the new athletics stadium was inaugurated on "Carl-Diem-Weg". After lengthy discussions about Carl Diem and his role in the Nazi regime, in 2008, following a decision of the District Council Cologne-Lindenthal and against the will of many GSU representatives, steps were taken to change the decades-old address of the university campus to "Am Sportpark Muengersdorf". 

In 2017 the GSU is celebrating its 70th anniversary.