Guantanamo has been a major political and national security headache for the president since he took office promising to close the prison within a year, a deadline that came and went without him ever setting a new one.
Obama made the change with clear reluctance, bowing to the reality that Congress' vehement opposition to trying detainees on U.S. soil leaves them nowhere else to go. The president emphasized his preference for trials in federal civilian courts, and his administration blamed congressional meddling for closing off that avenue.
"I strongly believe that the American system of justice is a key part of our arsenal in the war against al-Qaida and its affiliates, and we will continue to draw on all aspects of our justice system – including (federal) courts – to ensure that our security and our values are strengthened," Obama said in a statement.
"Going forward, all branches of government have a responsibility to come together to forge a strong and durable approach to defend our nation and the values that define who we are as a nation."
The first Guantanamo trial likely to proceed under Obama's new order would involve Abd al-Rahim al-Nashiri, the alleged mastermind of the 2000 bombing of the USS Cole. Al-Nashiri, a Saudi of Yemeni descent, has been imprisoned at Guantanamo since 2006.
Defense officials have said that of around 170 detainees at Guantanamo, about 80 are expected to face trial by military commission.
On Monday, the White House reiterated that the administration remains committed to eventually closing Guantanamo – which is on a U.S. Navy base – and that Monday's actions were in pursuit of that goal. But the outcome Obama wants seemed even more distant.
Critics of the military commission system, which was established specifically to deal with the detainees at Guantanamo, contend that suspects are not given some of the most basic protections afforded people prosecuted in American courts and that serves as a recruitment tool for terrorists.
