The underground areas found within the walls of the crusade church particularly attracted the attention of the Franciscans. This was a grotto that contained a series of pear-shaped silos and a very large cistern, connected to the exterior by a stairway cut into the rock. It seems that it is the result of a subsequent rearrangement of this area of the village, perhaps of the Byzantine era. These were the first remains of the village to come to light: the remaining part was found in the digs of 1930, intended for the construction of the new monastery, and in 1955, for the building of the Shrine of the Annunciation.
On the surface of the rock, a small bath was found, probably of the Byzantine era, approximately two metres square which, together with a column, at the steps leading down to the grotto and a wall found below the crusade apse, was oriented differently from the crusade church. For this reason, it is interpreted as part of an older building.
The bath dug into the rock, similar to the one that was later unearthed in the church of the Annunciation, has a stairway, with seven steps leading down to the south side. The steps and base are covered in simple mosaic decorations of black squares on a white background. There is a circular recess in the base of the bath in the north western corner of the bath, which probably served to collect water. The walls of the bath are plastered.
The bath and underground environments were studied by P. Bagatti and P. Testa: the hypothesis was that this area was used for Jewish-Christian baptism ceremonies. Evidence for this includes the cistern, used to provide the baptism water, the grotto, set up for the preliminary initiation ceremonies and lastly the bath where those baptised were immersed in water. The hypothesis, however, is not deemed valid by a number of academics such as Taylor, who is more inclined to the theory of an agricultural role of the bath or the grottos, ascribable therefore to a byzantine press. This hypothesis also comes from the observation of the mosaic covering of the bath, which is the typical cladding of baths used for oil pressing, and is, at least apparently, lacking in religious symbols.