Geren joined the Department of Defense in September 2001 to serve as Special Assistant to the Defense Secretary with responsibilities in the areas of inter-agency initiatives, legislative affairs and special projects.
On July 29, 2005, Bush appointed Geren the acting United States Secretary of the Air Force, a position he served in until the confirmation of his successor Michael Wynne in November 2005.
Geren was the 28th Under Secretary of the Army, a post he assumed on February 21, 2006, following his nomination by President George W. Bush and confirmation by the United States Senate. As the Undersecretary, Geren was the Army's No. 2 civilian leader. He served as the deputy and senior adviser to the Secretary of the Army and was Acting Secretary in the absence of the Secretary.
In March 2007, Geren was named Acting Secretary of the United States Army by Defense Secretary Robert Gates, after Army Secretary Francis Harvey resigned amidst the scandal at Walter Reed Army Medical Center. On July 16, 2007, Geren was confirmed by the Senate as Secretary of the Army.