Both treasury rooms of Collegium Maius hold the most valuable University memorabilia.

The University collection has a tradition beginning six centuries ago and still alive up to the present day. Many generous donors, both scholars and alumni, have made it possible for today's visitors to behold extraordinary works of art and handicraft, scientific instruments, and the keepsakes of the eminent and famous.

The most valuable objects are kept in the First Treasury vault. Rector insignias include the so-called Queen Hedwig’s sceptre (made after 1403), the sceptre of Cardinal Zbigniew Oleśnicki (ca. 1454), the sceptre of Cardinal Fryderyk the Jagiellon (end of the 15th c.), a golden chain (6th c.), and two rings (respectively 17th century and 1900). A special place is taken up by a mechanical armillary sphere known as  ‘The Golden Jagiellonian Globe.’ Dating to the 16th century, it was a gift presented by Prof. Jan Brożek. On the globe's surface beneath the armillary sphere, one can see America, one of the first such depictions in the history of globe cartography.

The display case mounted on the wall contains facsimiles of the Jagiellonian University foundation charters: the first one issued by Casimir III the Great (on 12 May 1364) and by Władysław Jagiełło (on 26 July 1400) which were reconstructed from photographs of the original documents destroyed during the Second World War.

The second part of the Treasury features a plethora of exhibits (15th-19th century): tableware, ceramic art, liturgical vessels, judaica, and, since 2018, a collection of objects commemorating the 100th anniversary of Polish independence. Additionally, this section of the Treasury presents the newest assets of the Museum collection: film awards donated by the film director Andrzej Wajda, a gold Olympic medal won by Robert Korzeniowski (2004), and the Nobel Prize medal bequeathed by Wisława Szymborska (1996).