At the base of the chapel's walls on the west end, the walls of the late 4th-century church are clearly visible on three sides. Like the early church, the modern chapel incorporates a large portion of the stone "table of Christ" (Latin: Mensa Christi) at the altar. This is where Jesus is believed to have served his disciples a fish breakfast after they landed on shore (John 21:9).

On the lake side of the church are the rock-cut steps mentioned by Egeria as the place "where the Lord stood." It is not known when they were carved, but it may have been in the 2nd or 3rd century when this area was quarried for limestone.

Below the steps are six heart-shaped double-column blocks known as the Twelve Thrones, which can be under water when the lake level is high. Originally designed for the angle of a colonnade, they were probably taken from disused buildings and placed here to commemorate the Twelve Apostles. The association likely derived from Luke 22:30: "You will eat and drink at my table in my kingdom, and you will sit on thrones to judge the twelve tribes of Israel."