The woman, known only as Nasim A., was expelled from Turkey with another woman and was detained at Frankfurt airport on Friday, the federal prosecutor's office said.
Turkey began deporting foreign jihadists on Monday and has criticised Western countries for refusing to repatriate their citizens who left to join IS in Syria and Iraq.
The Federal Prosecutor accuses Nasim A of having gone to Syria in late 2014 to live on IS territory.
She married an IS fighter in early 2015 and later settled in Iraq.
The woman is said to have taken care of the household and received around USD 100 a month in cash so her husband could be available for the jihadist group. She owned a Kalashnikov assault rifle.
The couple later went to back to Syria, where she was arrested in early 2019 by Kurdish security forces.
She was on Saturday to appear before the Federal Court which could issue a formal arrest warrant and order her detention on remand.
Turkey on Thursday also deported a man with suspected radical Islamist connections and his family to Germany.
Berlin city authorities said the man was arrested on arrival.