Mounir al-Motassadek, a 28-year-old Moroccan citizen living in Germany, becomes the second person to be charged in relation with the 11 September attacks.
He is charged by the German authorities with more than 3,000 counts of accessory to murder and belonging to a terrorist group.
Mr Motassadek is alleged to have helped members of the Hamburg cell of Osama Bin Laden's al-Qaeda network, blamed for hijacking four airliners and crashing them into targets in the US.
He was said to be responsible for supporting the suicide pilots while they were in America and arranging and financing their activities, including paying for flight schools in Florida.
Mr Motassadek had power of attorney over a bank account in Hamburg. Investigators say money in an account in Florida set up by Mohammed Atta, the alleged ringleader of the attackers, was traced to this account.