The archaeological data thus suggest a period of non-occupation, possibly a consequence of the Arab invasion. This could not have happened at the outset of the invasion (in AD 641), because a published papyrus (not in the Oxyrhynchus collection) refers to the city as active in AD 644/5. There was a revolt against the Arabs in AD 645/6 at Alexandria; perhaps something similar happened in Oxyrhynchus, and was ruthlessly put down. From the fourth century AD, Oxyrhynchus developed into a noted centre of Christianity. We learn from the writer Rufinus that there were 12 churches there early in the fifth century; he also tells us that the local bishop told him of the presence there of 10,000 monks and 20,000 nuns! Nevertheless the figure of 12 churches agrees well with a figure of 40 or more by the next century, supplied by a papyrus document of AD 535-6. However, if a clash of religions were responsible for such a revolt, Oxyrhynchus was not alone in its strong Christianity, and it is odd that the town should have been so singled out for repression. Hermopolis, for example, not far to the south, had numerous churches, among them a 5th century basilica church around 150 feet in length, and this town presents continuing documentation (including bilingual documents, Greek-Arabic) through the period of non-occupation at Oxyrhynchus.
A link between these various factors may be supplied, perhaps not altogether fancifully, by the early medieval Arabic epic Kitab Futuh al-Bahnasa al Gharra, the conquest of Bahnasa, the blessed, by Muhammad ibn Muhammad al-Muizz, which survives in four manuscript copies; a translation into French of the oldest of the copies, in Cairo, was published in 1909. The Futuh al-Bahnasa supplies topographical data which are to some extent verifiable, for example that the Muslim army destroyed the principal Christian church and that the towns first mosque, that of Hassan ibn Salih (still there), was built on the site in the late 9th century AD. We are told in St.Matthews Gospel that Mary and Joseph fled from Judaea to Egypt with the baby Jesus, to escape Herods persecution. The Futuh al-Bahnasa tells us that they stayed at Bahnasa (Oxyrhynchus); the town became a major Christian centre as a result of this tradition. Alas, no papyrus document has yet been found that attests their visit.