The presbytery area matches the perimeter of the basilica in the Byzantine age. The view of the Grotto of the Annunciation can be enjoyed from the iron balustrade. Inside the ancient semicircular apse of the Byzantine church there is a space for the officiants. The altar is at the centre of the small aisle and faces the Grotto.
The walls and floor mosaics of the Byzantine church can be seen from beneath the balustrade. These mosaic works are extremely fragmentary due to structural transformations that the sanctuary was exposed to over the years. The mosaics to the south, framed by a woven geometric pattern, belong to the side aisle of the Byzantine church; those to the west, facing the Grotto, feature a crown made up of black and vermilion red tiles with a Constantine monogram bearing the Greek letters Chi-Rho, the first two letters of Christ’s name. Next, another image in the same mosaic is made up of black tiles on a white background, with the motif of the cosmic cross. These signs were already used by the first Christians as Christological emblems and their position on the floor suggests that the mosaic complex dates back to 427 AD, when the emperor Theodosius II forbid the depiction of crosses on the floor to prevent the sign of redemption from being trodden on.