In 2002, the Theology section of the seminary became a directly affiliated Institute of the Pontifical Urbaniana. In July 2014 the Philosophy section too became an directly affiliated Institute of the Pontifical Urbaniana Univeristy, Rome.
The Pontifical Urbaniana University confirms the education quality every five years, and renews the affiliations with St. Mbaaga Major Seminary.
Currently the seminary is in the process of applying to the Goverment of Republic of Uganda to be fully accredited as a degree awarding institution in Uganda.