He served first in Berlin and from 1989 until 1991 he served in Northern Ireland, where he was Mentioned in Despatches. He became commanding officer of 1st Battalion The Black Watch (Royal Highland Regiment) in July 2003 and in that role was deployed to Iraq for Operation Telic in Summer 2004. Towards the end of the tour, Cowan led his Battalion during Operation BRACKEN, seeing action during the Second Battle of Fallujah, for which he was appointed an Officer of the Order of the British Empire. He became Chief of Staff for 3rd (UK) Division and was deployed to Iraq as Chief of Staff for Multi-National Division (South East) from July 2006 until January 2007.