His wife, a German convert to Islam, is already on trial over the case.
The man, identified only as Taha A.-J. in line with German privacy laws, faces charges of murder, membership of a foreign terrorist organization, genocide, crimes against humanity, war crimes and human trafficking, federal prosecutors said.
He allegedly joined the Islamic State group in 2013 and bought the girl and her mother as slaves in 2015. He and his wife, Jennifer W., allegedly left the girl chained outdoors at their home in Iraq as a punishment and she died of thirst.
Jennifer W. went on trial in Munich last April, charged with murder, a war crime and membership in a terrorist organization. Those proceedings are currently scheduled to last until mid-May.
Taha A.-J. was arrested in May last year in Greece and extradited to Germany in October. The indictment was filed Feb. 14 at the state court in Frankfurt. It wasn't immediately clear when a trial might open.