The site the church resides on was given to followers of Francis of Assisi in 1224. The foundation stone was laid by Premysl Ottokar II in 1276. Duke Albrecht II. later supported the building process, especially the main portal. The gothic Ludwigschor was built from 1316-1328 and used as a mausoleum in the 14th and 15th century. The church was finished in 1350.
The top of its tower was damaged during the first Austro-Turkish war, had been restored afterwards, but was destroyed again during the second Austro-Turkish war. Then, the top was replaced by a flat roof.
When Joseph II gave the church to Italy as a present, they transferred the name Maria Schnee ("Maria snow") from a nearby chapel to the church, tearing down the chapel.
There is a life-sized copy of Leonardo da Vinci's The Last Supper on the church's northern wall. It is a mosaic made by the Roman mosaic artist Giacomo Raffaeli which was ordered by Napoleon I in 1809, but it took so long to finish that in the end, Napoleon was not emperor any more. Francis II of Austria bought it, wanting to install it in the Belvedere in Vienna. As it was too large for the building, it was set up on the north wall of the church where it remains to the day.