The Grotto is entered by descending the stairs to the right of the iconostasis. Here the space is very narrow and restricted and the walls, which were originally irregular, form an almost-rectangular perimeter. The natural walls of the cave, decorated in the Constantine period, were covered with marble during the Byzantine period.

The Altar of the Nativity only began to be venerated in the Byzantine period when this space was created to commemorate the precise place in which Jesus had been born.

The current structure has been totally modified from that which was described by the pilgrim John Phocas and Abbot Daniel in the 12th century. Two red stone columns, and the inscription “Gloria in excelsis Deo et in terra pax hominibus”, overlook the altar, above which are representations of the Virgin and the Child in swaddling clothes, the scene of the washing, and that of the coming of the shepherds.

Beneath the altar is a star with the inscription “Hic de Virgine Maria Iesus Christus natus est” in memory of the precise spot of the Nativity. To the right of the altar is the place where Mary laid Jesus in the manger, also known as the Crib. At this point in the Grotto the floor is lower and the space is made up of columns similar to the Byzantine ones in the nave of the church, and by the remains of two Crusader columns.

In front of the Crib is a small altar dedicated to the Magi, where the Latins celebrate Holy Mass. The structure of the Crib is not the original one but is the result of alterations necessitated by the continuous wear and tear of time and the passage of pilgrims.

Following the fire of 1869 the walls of the Grotto were covered with asbestos to prevent further fires, a donation from the President of the French Republic Marshal Mac-Mahon in 1874. Below this covering the original Crusader marble is still visible, while above it can be seen wood panel paintings of limited artistic value.