Following the outbreak of the Irish Rebellion, Moore's house at Mellifont was captured on 21 November 1641 as a prelude to the rebels' Siege of Drogheda. Moore was one of the leaders of a relief force from Dublin that lifted the siege in March 1642. He and  Sir Henry Tichborne then marched on Dundalk and took the town. Tichborne became Governor of Dundalk and Moore returned to Drogheda.