The church which originally stood at the site of the present Cathedral (Stolnica), which is also referred to as the Church of St. Nicholas (Cerkev sv. Nikolaja), was a Romanic church with three naves, whose earliest mention was in 1262. After the fire of 1361 it was re-vaulted in Gothic style. When the Diocese of Ljubljana was established in 1461, the church underwent several alterations and a number of extensions were added to it. In 1469 it was probably burnt down by the Turks. In 1701 it was pulled down.

Between the years 1701 and 1706, a new Baroque hall church in the shape of the Latin cross with side chapels was built by the Jesuit architect Andrea Pozzo. Originally painted on the arch above the crossing was a fake dome, while the present real dome was only built in 1841. Apart from the frescoes by Giulio Quaglio painted from 1703 to 1706 and from 1721 to 1723, the surviving Baroque interior decoration notably includes the statues of four bishops of Emona by the sculptor Angelo Putti, which were built beneath the beams of the dome between the years 1712 and 1713, Putti's 1715 painting of Dean Janez Anton Dolnicar, who initiated the rebuilding of the church in 1701, the altar angels in the left part of the nave, sculpted by Francesco Robba in the period from 1745 to 1750, and the altar angels in the right part of the nave, which were sculpted by the brothers Paolo and Giuseppe Groppelli in 1711.

A host of other pieces of art were added later. One of the more interesting ones is the dome fresco painted by Matevž Langus in 1844. The most outstanding 20th century additions include the main entrance door, which shows the history of Slovenia and was on the 1250th anniversary of Christianity in Slovenia created by the sculptor Tone Demšar, and the side doors by the sculptor Mirsad Begic, which feature portraits of bishops.