On 1 October 2004, the University of Oldenburg was the first university in Lower Saxony and one of the first in Germany to switch its degree programmes almost completely to Bachelor's and Master's degrees.

The new degree programmes had been under discussion for years. They replaced almost all Diplom, Magister and state examination degree programmes in Germany. In 1999, the education ministers of 29 European countries decided in Bologna to standardise university degrees and introduce the credit point system (ECTS). This was intended to facilitate the recognition of degrees and international student exchanges. The university president at the time, Prof Dr Siegfried Grubitzsch, called the changeover the "biggest university reform since Humboldt". However, there was also a lot of criticism: the reform was accused of "schooling" the degree programme, providing too many examinations and leaving students with too few options. As a result, several adjustments were made to reduce the burden.

School V - School of Mathematics and Science was particularly quick in its implementation. As early as the 2005/06 winter semester, all of its then 16 Bachelor's and Master's degree programmes were accredited, i.e. recognised as fully-fledged degree programmes. This made it the first School in Lower Saxony to offer exclusively the new Bachelor's and Master's degree programmes. Computer science students have even been able to study with a Bachelor's degree since 2001.

As of 2024, the University of Oldenburg offers 17 subject Bachelor's degree programmes, 30 two-subject Bachelor's degree programmes, 82 teacher training Master's degree programmes and 50 subject Master's degree programmes as well as the State Examination in Human Medicine. In the examination year 2023, around 2,800 students graduated from the University of Oldenburg.