After the 2001 election, prime minister Tony Blair offered McDonagh the position of Parliamentary Undersecretary of State for the Communities. She declined the offer and remained a backbencher. After the May 2005 general election, she served as PPS to Dr. John Reid while he served as Secretary of State for Defence and from May 2006 to June 2007 Secretary of State for the Home Department. She was appointed to the position of Assistant Whip in June 2007 in the re-shuffle brought about by Gordon Brown becoming Prime Minister.