This church is where the Universal Council of 431 AD convened. It is the first church to be built in the name of the Virgin Mary and is often called as the Double Church since one part of the church was for Mother Mary and the other was for John the Apostle. The structure was used as an educational center for Ephesian Christian priests and also a public meeting house.

195 Bishops participated in the Universal Council when it was held at the church. The council discussed important church issues, such as the divine and human nature of Jesus Christ. The bishops heavily debated the idea that Mary gave birth to God since Christ was of both God and man. The idea was firmly accepted by some bishops and strongly contested by others. The Bishop of Constantinople and his supporters thought that the term “Mother of God” would threaten the depth of the respect for God and therefore petitioned for Mary to instead be called “Mother of Christ.” The Patriarch of Alexandria defended the understanding that Jesus Christ had one personality but two entities and therefore Mary should by right be called the “Mother of God.” The Patriarch of Alexandria prevailed and the council confirmed that Mary was the Mother of God.

The Church of Mary was built during the reign of Constantine the Great and clearly shows the architectural style of the time. It is a classical rectangular basilica with a large atrium entrance. The floor of the atrium is covered with marble blocks that were brought from all over Ephesus. The structure has three naves and the spaces between naves are colonnaded. On the eastern end of the middle nave is a wide apse with postophorion chambers on either side where ritual articles would have been. On the northern side of the atrium is a niched octagonal baptistery a marble covered chamber. A pool in the center of the floor would have served as a baptism area for adults. It is one of the best-preserved baptism areas of Asia Minor still visible. The narthex was ornamented with mosaics, rosettes and crosses.

The church was destroyed as a result of the Arab raids in the mid – 7th century AD but was used as a sacred site until the 11th century. Empty areas to the north and south of the church were used as graveyards during this time.