[3] Baldwin I, the first titled Crusader king of Jerusalem, banished his wife Arda to the old Benedictine convent which still existed here in 1104.

It was erected near the remains of the Byzantine basilica, over the site of a grotto believed by the Crusaders to be the childhood home of the Virgin Mary, mother of Jesus.

In 1192, Ṣalāḥ ad-Dīn converted the building into a madrasa (Islamic educational institution),[3] known as al-Madrasa as-Salahiyya (of Saladin),[5][6] as is still written in the Arabic inscription above the entrance.

In 1856, in gratitude for French support during the Crimean War, the Ottoman sultan Abdülmecid I presented it to Napoleon III.

The Byzantine basilica was partly stretched over two water basins, collectively known as the Pools of Bethesda, and built upon a series of piers, one of which still stands today in its entirety.

In 1862, the French architect Christophe-Edouard Mauss was dispatched by his government to Jerusalem with the special assignment of restoring the time-damaged church.

In 1996, during Jacques Chirac's visit to Jerusalem, the French president refused to enter the church until Israeli soldiers who accompanied him left.

Similarly in January 2020, French President Emmanuel Macron was involved in an altercation with Israeli security officers at the church.