UMB comprises six faculties that differ in character and history, each retaining substantial autonomy on financial and institutional affairs.

In the 1850s and 1860s, the Catholic grammar school with Slovak as a tuition language became an important center of education in the Kingdom of Hungary.

In the school year 1856–57 the first Teacher's Preparation Study was founded in Besztercebánya, where Slovak language was taught together with German and Latin, thanks to the bishop Štefan Moyses.

In the school year 1949–50, a branch of the Faculty of Education, Slovak University of Bratislava, was established in Banská Bystrica.

The Matej Bel University has traditionally been a decentralized institution, with governing authority shared among its academic faculties.

The Governing Council is the unicameral legislative organ of the central administration, overseeing general academic, business and institutional affairs.