Moussaoui on Friday said he understood he could be put to death for his role in the deadliest attacks against the United States on American soil.
US District Judge Leonie Brinkema accepted the plea, making the French citizen the lone person convicted in a US court for the 2001 attacks that killed nearly 3000 people.
Moussaoui, more subdued than in earlier court appearances during which he sometimes ranted at Brinkema, answered her questions politely.
"How do you plead?" the judge asked him for each of the six felony counts against him. Each time, Moussaoui answered, "Guilty."
But Sharif Basyuni, professor of international criminal law, told Aljazeera he believed Moussaoui was not fully aware of US law stating the criminal responsibility of a person taking part in a crime.
"Moussaoui has confessed he has committed another crime, mistakenly believing that his confession of another crime may clear his responsibility for taking part in the bigger crime that has been previously committed by other people," he added.