For at least 1,000 years, the monastery was the most popular destination for pilgrims in the region. The name of the monastery (Agioi Saranta - in Greek meaning Forty Saints) was transferred to the adjacent port city of Saranda. During the People's Republic of Albania (1944-1991) the monastery was used as a military site.

The monastery was probably founded during the reign of Byzantine Emperor Justinian (527–565 AD) and remained a shrine until the communist era in Albania (1944-1991)

The complex of the monastery included the basilica church as well as hostels for pilgrims and other guests, underground chambers, holy water springs and crypts. In the underground rooms there were 40 small chapels, each dedicated to one of the Forty Martyrs of Sebaste who were martyred during the Early Christian period. The complex was partially destroyed by the Ottoman Turks from the 15th century onwards, then reduced to ruins during the Second World War, before being demolished and being transformed into a military base in the 1950s during the atheistic campaign of the authorities of the People's Republic of Albania.

In spite of this, it still retains some religious importance for the local Greek Orthodox population and pilgrims continue to leave flowers here.