Abeer Talaat Fakhry, 26, was living with her Christian husband in the southern city of Assiut when she ran away from home, converted to Islam and "married" Muslim Yassin Thabet, the source said.
Hundreds of ultra-conservative Muslims known as Salafists attacked a church in the poor Cairo district of Imbaba on Saturday, spurred on by rumours that Fakhry had converted to Islam and was being held there against her will.
In subsequent clashes with Christians, 15 people died and more than 200 others were injured.
But the source said Fakhry was actually with her new "husband" in a house next door to the church and that she had fled when the clashes began.
The largest Christian community in Egypt is that of the Copts, in whose church divorce is extremely difficult to obtain.
There have been a number of cases in which unhappy women have left their husbands, converted to Islam and "married" Muslims, but those marriages are not recognised in law.
Hence, the charge that Fakhry had committed polyandry, or having more than one husband.
Claims that Christian women had converted to Islam, were kidnapped and being held in churches or monasteries have soured relations between the two communities for months.
Islam allows non-Muslim women to marry into the faith, but prohibits Muslim women from marrying outside of it.
Copts account for up to 10 per cent of the country's 80 million people. They complain of discrimination, and have been the targets of fairly regular sectarian attacks.
