Margalit (1987) excavated the North Church at Shivta and identified two principal building phases. He reported that "the first basilica was a monoapsidal church erected in the mid-fourth century A.D." Beneath the sealed limestone floor of this first phase, seven coins of the mid-4th century CE were recovered, providing a basis for dating the original construction. According to Margalit (1987), "after the first church was damaged, most probably by an earthquake, a new one was erected in the beginning of the sixth century A.D." He further suggested that the original pavement subsided during the event and that "a marble floor was laid at a higher level than the original pavement" during the second phase of construction.

Negev (1989) also interpreted the architectural remodeling of the North Church as the result of a major earthquake. He wrote that "a severe earthquake afflicted Sobata [Shivta]" and that the monoapsidal basilica suffered extensive damage. The structure was subsequently surrounded by high stone taluses, and the southern wall was reinforced by two strongly built chapels. According to Negev, this reconstruction marked the beginning of the second phase of the church, which was dated by a coin of Justinian (r. 527–565 CE) found in the fill behind the southern apse and dated to between 527 and 538 CE. Epigraphic evidence, including inscriptions dated to 506 and 512 CE, indicates that the remodeling began in the first decade of the sixth century.

Negev linked this destruction to earthquakes recorded in the later fifth and early sixth centuries, drawing on Kallner-Amiran’s catalog (1952). However, none of the proposed earthquakes were close enough to the Negev to produce major damage. On chronological and regional grounds, the hypothesized Negev earthquake of ca. 500 CE therefore remains a distinct possibility for the event that damaged the North Church and initiated its early sixth-century reconstruction.