Established in 1991 at Stična Cistercian Abbey as the Slovene Religious Museum, today the museum occupies a 2,000 square-metre space within a Renaissance-Baroque building known as the Old Prelature. The Museum of Christianity in Slovenia acquired the status of national public institution in 2006.

The first floor of the building houses the monastery's extensive collection of liturgical vessels, vestments and art works. Pride of place is given to facsimiles of the famous 12th-century Stična manuscripts and the Stična manuscript of 1428, one of the first written documents in the Slovene language, which were held in the Stična Cistercian Abbey Archives until the 18th century. The museum also houses the original literary works and correspondence of missionary and bishop F L Baraga (1797-1868), who in the 19th century worked among the North American Indians. The second floor of the museum houses the exhibition The history of Christianity in Slovenia and continues through approximately 1.700 years of history right up to the year 2000. The ground floor of the museum is used for occasional exhibitions. Recently a new restoration centre has been set up.