Rebuilt by order of the Emperor Justinian after the Samaritans revolt.
Historical and archaeoogical considerations for dating this phase prevent determining an exact date. The data and considerations were presented recently (2017) by Bacci:
Dendrochronological and radiocarbon analysis of the wooden architraves revealed that they can be dated to the year 605 +- 60 years, i.e. between 545 and 665 CE (Bernabei and Bontadi 2012, pp. 58 –59).
This building project is mentioned only in the Arabic Chronicle of Eutychius (Ibn-Batriq), Patriarch of Alexandria (9th c.), according to which the first building was pulled down by order of Justinian, since he considered it to be too small. The event took place after a Samaritan revolt. The emperor was not satisfied from the new building presented by his envoy to the Holy Land, and ordered to behead him.
Procopius does not mention it in his "Buildings". Hence, it might had started only after the compostion of this book was completed (ca. 554-560). But it can also be conjectured that Procopius’ silence about these works may be due to the Emperor’s disappointment about the final form of the first new building.
The Samaritan revolt mentiond by Eutychius might be that of 555/56, rather than that of 529/30. It may also be that the need for new works was prompted by some damage caused by the earthquake which devastated Palestine in 551.
Cyril of Scythopolis (ref.) hints that in 557 the narthex - a new distinctive feature of the reconstructed building, already existed.
According to Bacci (2017), it should be assumed that the building campaign was initiated after Procopius had finished his book, i.e. after 560 according to most scholars, or even earlier, around 554 –555 according to an alternative hypothesis. The reconstruction works at Bethlehem could therefore have started in the last years of Justinian’s rule and have lasted beyond his death in 565.
The triconch layout is first mentioned by Sophronius, Anacreontics XIX, 23–56 (603-4 CE).
The church remained unharmed by the Persians due to the wall mosaics on its facade, depicting the Adoration of Magi. This is mentioned in the Letter of the Three Patriarchs of the East to the Byzantine emperor Theophilos (9th c.).