Al-Bahlul is accused of preparing al-Qaeda recruiting materials, including a video glorifying an attack on the USS Cole warship in 2000, of videotaping the will of Mohamed Atta, alleged leader of the September 11, 2001 attacks, and of being a body guard to Osama bin Laden.
The charges of terrorism and murder carry a maximum sentence of life imprisonment.
In the first Guantanamo military tribunal, Salim Hamdan, a former driver for bin Laden, was found guilty only of "providing material support to terrorism" and sentenced to five months in jail, taking into account the years he had already spent imprisoned.
The military trials have been heavily criticised by defence lawyers and rights activists.
Jamil Dakwar, director of the ACLU Human Rights Programme, who is observing the trial, said "America deserves better than a system that is so incompatible with universal notions of fairness and justice".
"These commissions don't even resemble a legitimate justice system. They have become a farce in the eyes of the world."
Both major presidential candidates have said they will close the Guantanamo prison facility following the November 4 election.
About 255 suspected members of al-Qaeda, the Taliban and others have been imprisoned for as long as six and a half years without trial at Guantanamo, which once held as many as 600 detainees.