The 30-year-old electrical engineering student faces 3066 counts of aiding and abetting murder as well as being a terrorist organisation, Reuters reported.
Mzoudi, arrested in October 2002, could be imprisoned for up to 15 years. Fellow Moroccan and co-conspirator Mounir El Motassadeq was jailed in February in what was the first trial directly related to the 2001 attacks in the US.
"From early summer 1999 until September 11, 2001, he was a member of a terrorist organisation and helped the suspected terrorists commit murder and other crimes," prosecutor Matthias Krauss told the court as he read the indictment against Mzoudi.
Mzoudi, standing behind a thick pain of security glass, listened to the charges and spoke only to confirm his name, date and place of birth and marital status. Police blocked the road leading to the courthouse and a plethora of officers patrolled the building.
Though Mzoudi was first questioned by German investigators last summer when they raided an Islamic bookstore in Hamburg, he wasn't arrested until October.
An unidentified witness told police that Mzoudi had been at an Afghan training camps in 2000, together with Motassadek and Zakariya Essabar, another alleged member of the Hamburg cell.
Motassadek later testified that he had seen Mr Mzoudi in Afghanistan.
The 92-page indictment states that Mzoudi was briefed on the plot to attack US cities whilkst in Afghanistan.
It also accuses him of handling money transfers for one of the potential airline hijackers, arranging student housing in Hamburg for cell members and helping hide two of the attackers' whereabouts while they attended flight training in the US.
Defence lawyers are expected to argue that Mzoudi was simply being charitable to his fellow Muslims, and that he knew nothing of the impending atrocities.
Germany became a focal point of the war against terror after it emerged three of the men that piloted the suicide flights had been students in Hamburg.
Muhammad Atta, the accused ringleader of the attacks, attended the same Hamburg Mosque as Mzoudi.
The trial is expected to continue into 2004.