The site was purchased from the Georgian Orthodox Church in 1560 with permission of Sultan Suleiman the Magnificent of the Ottoman Empire, and the monastery was constructed in stages.

The monastery was built in several stages on a site transferred to the Franciscan Order from the Georgian Orthodox Church in 1558–59 by Sultan Suleiman the Magnificent.

[1] Official support for the construction of the church was provided by Austro-Hungarian Emperor Franz Joseph I during his visit to Jerusalem in 1869.

In 1932, two stories were added to the clock tower in honour of the 700th anniversary of the death of Saint Anthony of Padua.

Over the years, a Catholic school for boys and girls, a printing press and an organ workshop were built on the monastery compound, and are still in operation today.