The 32-year-old, identified as Thaer A., is charged with founding a terrorist group with four others in June and July last year.
A statement from the prosecutor’s office said he was acting “on the orders of Osama bin Laden”.
A.’s role was to handle money transfers, the statement said.
German authorities tracked him after monitoring Internet chatrooms during the surveillance of a Moroccan man who is now also being held on charges of supporting Al-Qaeda.
A. was arrested in Sweden on March 19 on a European warrant issued by Germany.