en-Nabratein presents a debated chronological sequence. Meyers et al. (2009) excavated what they designated as Synagogue 2 at en-Nabratein, subdividing its use into two phases within Period III (Late Roman, 250–350/363 CE). Meyers et al. (1982) dated Period III Phase a on the basis of ceramics and coins, ending this phase with the Eusebius’ Martyr Quake of ~306 CE, which they believed damaged the synagogue and prompted its reconstruction—the beginning of Period III Phase b.

Magness (2010) re-examined the excavation data of Meyers et al. (1982), focusing on stratigraphy and dating evidence. She concluded that only a single synagogue was ever built on the site, dating no earlier than the second half of the fourth century, with occupation continuing during the very centuries the original excavators considered abandoned. A coin dated 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. Additional evidence suggests a terminus ante quem in the later fifth century or even the mid-sixth century. An inscription records that the synagogue was built or renovated in 564 CE (Magness 2010). Meyers and Meyers (2010) responded, disputing Magness’s interpretation of the stratigraphy and chronology and arguing that sloping bedrock, lensed layers, later disturbances, and the misplacement of the 341–346 CE coin (found in fill rather than in the wall) complicate her reconstruction.