His monographs include Britain, Denmark-Norway and the House of Stuart, 1603-1660 (2000/2003); Network North: Scottish Kin, Commercial and Covert Associations in Northern Europe, 1603-1746 (2006) and the book The Terror of the Seas?
In 2014 he published the co-authored book (with Alexia Grosjean) Alexander Leslie and the Scottish Generals of the Thirty Years' War, 1618-1648.
He has edited several volumes including Scotland and the Thirty Years' War, 1618-1648 (2000) and with Alexia Grosjean Scottish Communities Abroad in the Early Modern Period (2005).
Murdoch was nominated for, and won, the Olof Palme Professorship in Peace Studies by Vetenskapsrådet (The Swedish Research Council) for the academic year 2013–2014.
In January 2023, Murdoch became head of the Military History Department (MHA), then a part of War Studies (IKVM).