In 603, Pope Gregory I commissioned the Ravennate Abbot Probus, who was previously Gregory's emissary at the Lombard court, to build a hospital in Jerusalem to treat and care for Christian pilgrims to the Holy Land. In 800, Emperor Charlemagne enlarged Probus' hospital and added a library to it. About 200 years later, in 1009, the Fatimid caliph al-Hakim bi-Amr Allah destroyed the hospital and three thousand other buildings in Jerusalem. In 1023, merchants from Amalfi and Salerno in Italy were given permission by Caliph Ali az-Zahir to rebuild the hospital in Jerusalem. The hospital was served by the Order of Saint Benedict, built on the site of the monastery of Saint John the Baptist, and took in Christian pilgrims traveling to visit the Christian holy sites.

The Hospital of St. John was therefore believed to have been founded shortly before 1070 in Jerusalem, as a dependency of the Benedictine house of the Church of Saint Mary of the Latins. The founding Amalfian merchants dedicated this hospice to St. John the Baptist, reflecting the pre-sixth century Basilica of the Crucifix in Amalfi dedicated to the Assumption. Shortly thereafter, a second hospice for women was founded and dedicated to Saint Mary Magdalene. The hospital, in the Muristan district of Jerusalem, was to provide care for sick, poor, or injured pilgrims to the Holy Land.