St. Paul University Dumaguete was granted autonomous status last May 16, 2016 and valid for three (3) years. The university is one out of two universities in Dumaguete to be given such. This award was given by CHED and accepted by the outgoing University President Sr. Nintha Lucilla Baldado, SPC and the incoming one, Sr. Joseline Lasala, SPC.

The university is also the recipient of the Fr. Theodore Murnane Research Commitment Award in recognition of its commitment to raise community awareness of the importance and relevance of health services. The award was given on June 21, 2017 in Cebu City.