The mosaics show an interesting point in the history of the church when figurative emblema was eliminated. The two periods of the mosaic show a transition from an earlier phase of simple designs towards a more complex and rich effect and the floor treated as a whole unit of ornament. The whole church and its annexes were paved with mosaics but for smaller areas such as the atrium. These pavements belong to three possible distinct periods. The first and second pavements are easier to date on grounds of style and execution while the third is dated on the basis of an inscription. The second pavement was laid over the northeastern chapel probably due to the decree of Theodosius II and Valentinianus in 472 (preserved in the codex of Justinanus). This decree forbade the use of the cross and other Christian symbols and called for their removal in cases where they were already made. Likely this is the reason a second pavement was layered on top of the first. Only a small section of the church apse mosaic has survived but remains indicate it continued towards the nave. Another small section of mosaics between the north-eastern nave corner and north aisle survived. The simple geometric style was favorite perhaps as a reaction to blatant pagan decorations. Instead, this late Roman type ornament was selected for the decoration of the church.
The inscription in the outer narthex indicates the church was enlarged and repaired in 486 C.E. The central and eastern part of the nave show repair of the mosaic done due to changes in the space structure. The earlier pavement lacks an inscription and is dated on internal evidence to the early 5th century. The central patterns in the nave and aisles accur for example at et-Tabgha (mid 5th century), Eleona church (5th century) supporting this dating. These common geometric patterns reemerge in the 7th and 8th century. Additionally, such "scale" patterns can be found outside of the holy land in Acholla Tunis in the Antonine period, Rehiems and at the Blantzy les-Fismes (first half of 4th century). This and other evidence indicates that the mosaic style was passed on from Africa towards Gaul and Germany.
Avi-Yona dates the first phase to in the late 4th or early 5th century while the second phase is dated to 486.