Ahmed Khalfan Ghailani, 36, a Tanzanian from Zanzibar, had been accused of conspiring in the 1998 al Qaeda bomb attacks on U.S. embassies in Kenya and Tanzania that killed 224 people.
The jury, which deliberated for five days, found him guilty of one relatively minor charge of conspiracy to damage or destroy U.S. property with explosives. He faces a mandatory minimum of 20 years in prison and a maximum of life.
Ghailani was cleared of 276 murder and attempted murder counts, along with five other conspiracy charges.
It was a rare defeat for the U.S. Attorney’s Office in New York, which has a near perfect record in prosecuting terrorism cases.
Ghailani’s trial was being watched closely as a test of Obama’s approach to handling the 174 terrorism suspects held at Guantanamo Bay, Cuba, including Khalid Sheikh Mohammed, the accused mastermind of the Sept. 11 attacks.
Obama has vowed to close the U.S. prison at Guantanamo Bay amid international condemnation of the treatment of detainees, but he has run into political resistance at home.
His administration has adopted what it calls a flexible approach in dealing with terrorism suspects, favoring military tribunals in some cases and civilian trials in others.
Most Republicans say all terrorism suspects should be tried in military tribunals. U.S. Attorney General Eric Holder has defended the option to use civilian criminal courts.
“We respect the jury’s verdict and are pleased that Ahmed Ghailani now faces a minimum of 20 years in prison and a potential life sentence for his role in the embassy bombings,” Justice Department spokesman Matthew Miller said in a statement.
Ghailani was held in CIA custody after his July 2004 arrest in Pakistan, moved to Guantanamo Bay in late 2006, and transferred to New York in June 2009 to stand civilian trial.
The government accused Ghailani of buying seven gas cylinders used in the bomb and the truck used to transport it. Prosecutors said Ghailani flew to Pakistan along with senior al Qaeda operatives on the day before the bombings, and that a blasting cap was found in a cupboard in his room.
Defense lawyers called Ghailani a naive boy who was tricked by al Qaeda and they denied Ghailani ever took the flight to Karachi.
