Although Meyers, Strange, Meyers, and Hanson (1979) interpreted the destruction at the end of Stratum VIa as resulting from the Eusebius' Martyr Earthquake (~306 CE), their chronology remains debated. Magness (2001a) conducted a detailed re-examination of the stratigraphy published in Meyers, Meyers, and Strange (1990) and concluded, based on numismatic and ceramic evidence, that the earliest synagogue was built on the site no earlier than the second half of the 5th century CE. While she agreed that earthquake destruction was evident in the excavation, she dated this damage to sometime after the site’s abandonment in the 7th or 8th centuries CE. Strange (2001) and Meyers (2001) rebutted Magness (2001a), to which Magness (2001b) replied. One point of agreement among these scholars is that earthquake destruction evidence is indeed present.

Eric M. Meyers in Stern et al. (1993 v. 2) also discussed this earthquake, noting that although the Eusebius' Martyr Earthquake (~306 CE) apparently did significant damage to the structure, "the stylobates were shored up and other repairs undertaken to make the Period II building sturdier".