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, Agence France-Presse reports.
After rumors circulated that Fakhry was being held against her will in a church in the poor district of Imbaba on Saturday, her Muslim partner then reportedly rallied hundreds of Salafists, or ultra-conservative Muslims, who attacked the church.
AFP reports that "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 recognized in law."
Hence, the charge that Fakhry had committed polyandry — a form of polygamy where a woman has more than one husband.
The Copts form the largest Christian community in Egypt, accounting for up to 10 percent of the country's 80 million people. They complain of discrimination, and have been the targets of fairly regular sectarian attacks.
Divorce is extremely difficult to obtain in the church.
Islam allows non-Muslim women to marry into the faith, but prohibits Muslim women from marrying outside of it.
An official told The Associated Press that Fakhri would be held 15 days for questioning.