In the later sequence of the Great Temple precinct, Joukowsky (2007:34–35) describes a sixth-century phase of renewed structural failure and contraction, noting that “in Site Phase XI there is further collapse that possibly postdates the fifth century CE.” Some of the collapses she records may reflect long-term degradation, while others could plausibly be attributed to a sixth-century seismic shock.

In the Propylaeum she records that "major collapses continue," suggesting that the formal entrance to the sacred complex was no longer structurally secure. In the Lower Temenos there is "continued accumulation of fill and the West Entry Stairs go out of use," reflecting both collapse and progressive abandonment of circulation routes. On the eastern side, she reports that "the East Triple Colonnade collapses along with the East Exedra’s entablature." The failure of both the colonnaded façade and its overlying architectural superstructure signals major structural breakdown in one of the precinct’s most formal architectural settings. In the Upper Temenos she similarly notes "further collapse," followed by "the accumulation of fill after disuse of the canalization system," together with "areas of localized burning." These observations collectively depict a sixth-century landscape dominated by fallen architectural elements, clogged drainage, and piecemeal adaptation rather than coordinated rebuilding.

The Roman-Byzantine Baths provide the clearest marker of terminal decline. Joukowsky (2007:34-35) states that "modifications take place in the Roman-Byzantine Baths and a final collapse occurs after which the bath site is finally abandoned," adding that it is "unlikely that the complex functioned beyond the mid sixth century." She concludes that this stage marks "the terminal phase of site occupation" for the Great Temple precinct. Although she refers to the the termnal phase ending in the mid sixth century, the date of this final collapse was probably the late 6th century as the late 6th century Inscription at Areopolis Quake is more plausible candidate for causing this damage than the distant 551 CE Beirut Quake.