en-Nabratein presents a debated chronological sequence. Meyers et al. (2009) excavated what they identified as Synagogue 2 at en-Nabratein, dividing its history into two phases within Period III (Late Roman, 250–350/363 CE). Meyers et al. (1982) dated Period III Phase a using ceramics and several coins, concluding that this phase ended with the Eusebius’ Martyr Quake (~306 CE), which they believed damaged the synagogue and led to its reconstruction at the start of Period III Phase b. The end of Phase b is not clearly defined by material remains; ceramics and “an irregular supply of coins dating up to ca. 350 A.D.” provide the earliest possible date for its termination. The authors suggested that the close of Period III b likely resulted from a combination of causes, including the revolt against Caesar Gallus (350–352 CE), economic decline, and the great earthquake of 363 CE. By the later fourth century, they considered the site nearly abandoned until a third synagogue was established at the end of the Byzantine era in 564 CE, as indicated by an inscription.

Magness (2010) re-evaluated the reports of Meyers et al. (1982), focusing on stratigraphy and chronology. She argued that only one synagogue was built on the site and that it dates “no earlier than the second half of the fourth century,” coinciding with the period when the original excavators believed the site had been abandoned. A coin of 341–346 CE from the east wall and associated pottery provide a terminus post quem in the latter half of the fourth century for the synagogue’s construction. Other evidence points to a terminus ante quem in the later fifth century or possibly the mid-sixth century. An inscription also records that the synagogue was built or remodeled in 564 CE (Magness 2010). Meyers and Meyers (2010) responded, disputing Magness’s interpretation of the stratigraphy and chronology and emphasizing complications from sloping bedrock, lensed layers, later site disturbances, and the fact that the 341–346 CE coin was recovered from fill rather than the wall itself.