The Church of St. John, located at the southern foot of the castle hill, is the most magnificent of the buildings from the Byzantine Period. The historian Eusebius tells us that after the apostles were expelled from Jerusalem around AD 37 to 42, St. John continued his work in Anatolia from Ephesus. In this way we can understand when St. John and Mary, the mother of Jesus, who had been entrusted to him by her Son, came to Ephesus. 

After the martyrdom of St. Paul, St. John wrote his gospel and labored in his ministry to the churches in the area. After his death, he was buried in the church that was built to remember him. After Christianity came into its own in the fourth century, a wooden-roofed basilica was built over the site of his grave. The basilica was cross-shaped with five naves and a narthex. The grave of St. John is purported to be under the central nave.  Fortifications were built around the church in the 7th and 8th centuries at the time of Arab incursions into the area, giving it the appearance of an outer castle connected to the castle on the hill.

In the 14th century, after the Isabey Mosque was built near the church, the area became better known. It is visited today by numerous tourists thanks to the excavation work that is still going on.