Al-Nashiri will be arraigned before a military judge on Wednesday, after having been held in a network of clandestine CIA prisons and a hyper-secretive section of Guantanamo.
The Cole bombing killed 17 sailors and wounded 37. The charges against Nashiri include murder in violation of the law of war, which could carry the death penalty.
The trial is not expected to take place for months, or even years, due to an expected lengthy legal battle over the evidence, according to AP.
Lawyers for al-Nashiri say that a legitimate trial will be impossible since he was subject to torture while in custody. "By torturing Mr. al-Nashiri and subjecting him to cruel, inhuman and degrading treatment, the United States has forfeited its right to try him and certainly to kill him," his defense team said.