According to the Gospel of John, as Jesus was hanging on the cross, He presented His beloved disciple John with the care of His mother, Mary. Four of six years after the death and resurrection of Jesus, St. John and Mary are thought to have come to Ephesus and stayed on the site of what is not the Church of the Council of 431. Later, John took Mary to a house he had built on Nightingale Mountain. This house where Mary is thought to have spent her last days was forgotten in time and fell to ruin. In the Middle Ages it was often claimed that the house was found but to no definite result.

In 1878 German nun Katherina Emmerich talked about the location of the house in a book by Clementi Brentado and interest was revived. In 1891 the Lazarist priest Eugene Poulin, who was head of Izmir College, sent a group under priest Yung to find out if what was being claimed was true. The group explored the mountains south of Ephesus and came upon the house now know as the House of Mary.

Katherina Emmerich (1771-1824) had never left her hometown in all her life, was in a trance when making her explanation of ht house's location. After this discovery, Eugene Poulin printed a number of things to increase interest in the find. The event was heard around the world. Many religious investigators shared the same conclusion. Izmir Patriarch Monsignor Timoni visited the site and gave permission for conducting services on the site in 1892. Pope John XXIII proclaimed the house a pilgrimage site, quieting all controversy over the site. In 1967 Pope Paul VI came, and Pope John Paul II came in 1979, both adding to the significance of the site.