US District Judge Leonie Brinkema, who has cautioned Zakarias Moussaoui several times, issued an order on Friday revoking the right she had originally granted last year.
She said the court-appointed lawyers who had been ordered to assist Moussaoui would again represent him.
Brinkema warned Moussaoui on 6 November that he faced losing the right to defend himself if he continued to file "further frivolous, scandalous, disrespectful or repetitive pleadings".
She said she also sent him a letter on 7 November informally reminding him of the sanctions he faced.
But Moussaoui continued to make filings to the court that she said were repetitive and included "contemptuous language" that would never be tolerated from an attorney.
"Based on the defendant's repeated violation of orders of this court, he has forfeited his right to represent himself any further in this case"
Judge Leonie Brinkema
"Based on the defendant's repeated violation of orders of this court, he has forfeited his right to represent himself any further in this case," Brinkema wrote.
Frank Dunham, the public defender who will head Moussaoui's defence team, called the ruling a mixed blessing.
"It makes life harder and easier at the same time," he said. "It means you could be trying a case for a client who hates you. At the same time, you know your destiny."
The US attorney prosecuting the case refused to comment.
Moussaoui, 35, is a French citizen of Moroccan descent who is the only person facing trial in the United States in connection with the September 11 attacks.
Although not an attorney, Moussaoui asked Brinkema early in the court proceedings if he could fire his court-appointed lawyers and represent himself.
He claimed the lawyers were part of a conspiracy by the government and the judge to kill him.
Brinkema granted his request in June 2002, despite protests from Moussaoui's lawyers that their client was not mentally competent.
Moussaoui then began filing numerous handwritten pleadings with the court, many of which included inflammatory language about US officials and his lawyers.
Earlier this year Moussaoui said that he wanted to torture US Attorney General John Ashcroft.
"Ashcroft must be sent to Alexandria jail so I can torture him. After all torture is now part of the American way of life," Moussaoui wrote.
In previous filings, Moussaoui has called his lawyers a horde of bloodsuckers and a "death team", and accused Brinkema of being biased and having a possible mental disorder.
"(John) Ashcroft must be sent to Alexandria jail so I can torture him. After all torture is now part of the American way of life"
He regularly lashed out at the US government for wanting to conduct a "show trial" before moving on to kill him.
After hundreds of such filings, Brinkema ordered all Moussaoui's filings to be put under seal until they could be vetted for inflammatory language or possible hidden messages.
They would then be unsealed with some parts blacked out.
The judge said in an order last year that Moussaoui was trying to use the court as a vehicle through which to communicate with the outside world, and as a result she would keep some of his writings completely under seal.
Brinkema has put the trial on hold until appellate courts resolve whether Moussaoui can question al-Qaida suspects held in captivity. He faces a possible death sentence if convicted.
Moussaoui, who was being held on immigration charges on September 11, has denied being a part of the attacks although he has admitted to being a member of al-Qaida.