This church is located to the south of the fortress in the district of Selcuk. The Church of Ephesus was founded by St. Paul and carried on by St.John. According to St. John's Gospel Christ had entrusted his mother to St. John before being crucified. Seeing their lives in danger in Jerusalem St. John came to Ephesus with the Virgin Mary. Ephesus was one of the most modern and tolerant cities of the time. In those days people of all religions could worship their cult without any difficulty. Therefore their coming to Ephesus was not accidental.
In spite of his old age St. John tried to propagate the new religion. When he died he was buried according to his wishes in the church of which we see the remains today and in the 4th The Church of St. John century a small basilica was constructed on his tomb. And in the reign of the Emperor Justinian the present church was built.
The Church of St. John was of a size and beauty to compare with the Temple of Artemis lying to its south. At its west end it had an atrium of which the like is rarely to be seen. The square shaped atrium was surrounded by porticoes on three sides and the outer side was covered with parapets and turned into a promenade. The inner side of the wall built at the west end by removing the slope of the hill was designed to form a cistern. The cistern is at present repaired. To the east of the atrium was an exonarthex built at a later period and after that the narthex covered with five little cupolas.
From the narthex three doors provided entrance to the main part of the church. These doors were the beginnings of three naves. According to an old tradition the middle nave was built larger that the others. After the naves and before reaching the apse transepts were built on the sides. The naves were covered with six large domes. The tomb of the saint lay in the tomb chamber underneath the middle dome. The top of the tomb was raised from the ground and was covered with mosaics. These mosaics were taken away one by one by the devoted and new ones made according to the excavation drawings were put in their place. The entrance of the tomb chamber was by means of a narrow staircase on the side of the apse. The belief that a healing powder came out of a little hole near this brought many pilgrims here to smell it in the Middle Ages. The tomb chamber was surrounded by an architrave with coloured columns and inscriptions.
The raised walk in the shape of a wall led to the ambo of which only traces remain today. In 1967 the pope prayed in this church. To the north of the edifice the building covered with a roof is a chapel constructed in the 10th century. In the apse of the chapel are frescoes of Christ in the middle with two saints on either side. Of these the one on the right is St. John. The polygonal and two storeyed building right near the chapel was a domed treasury building. In the niches visible in the walls were kept the sacred objects of the church. The mosaics and the small altar standing on them which can be seen after these niches were built in the 12th century by the crusaders. When the mosaics were removed for repair fragments of gilded capitals were found underneath.
The hexagonal baptistry of the church stands next to this. Between the baptistry and the north nave there is a fountain of fine workmanship. A part of the church was excavated in 1920-21 and the other part was excavated later. The two tiers of columns in the north nave were erected during the first period of work. On the columns of the first floor there are the monograms of the Emperor Justinian and his wife Theodora. The edifice is being restored at present by the Museum of Ephesus. Part of the restoration expenditures are met by the Quadman family from the U.S.A.
The area on which the church stood took on the aspect of a fortress as its walls were strengthened and fortified with frequent towers against Arab attacks in the 7th and 8th centuries. The fortress had three gates. Of these the one on the west was excavated and restored whereas the excavation of the one on the east has not yet been undertaken. The gate on the south was called the Pursuit Gate. This gate was guarded by two tall towers. In the inner side there was a narrow courtyard. If the gate broke under the attacks the enemy would be destroyed in this courtyard by firing and shooting from the walls. The walls encircling the church extend as far as the fortress on the hill. At its east end the site of the earliest settlement in Ephesus was discovered. The fortress was built in the 5th century and was used until the 12th century with various repairs. It had two gates, one on the east and the other on the west. The interior has not been excavated yet. There are cisterns. a chapel and a small mosque in it.