Jordan volunteered to return to active duty to support the war in Iraq, and as a civil affairs officer with a background in military intelligence, was made the director of the Joint Interrogation Debriefing Center at Abu Ghraib prison.

In a report by Army Major General Antonio Taguba, Jordan was among several described as being "directly or indirectly responsible for the abuses at Abu Ghraib".

[5] A number of findings were made in their investigative report, with recommendations the authorities should take against the officers and enlisted soldiers implicated in the Abu Ghraib prisoner abuse, including Jordan.

In 2007, Jordan was tried by court martial on charges of failure to obey regulations, cruelty and maltreatment of detainees, dereliction of duty, making a false official statement, obstruction of justice, and discussing the investigation with others when ordered not to do so.

This admission contradicted his sworn testimony at a March 12, 2007 pretrial hearing in which he testified under oath that he had advised Jordan of his rights.

He further stipulated that military police were in charge of the November 24, 2003 weapons search which he had personally observed, and found no issues with.