With other royalists Nairne was captured by a detachment from General George Monck at Alyth, Forfarshire, 28 August 1651, and sent a prisoner to the Tower of London, where he remained till the Restoration of 1660. By Charles II he was appointed a lord of session, 1 June 1661, and was knighted; and on 11 January 1671 he was appointed to the court of justiciary. On 23 Jan. 1681 he was created a peer of Scotland by the title of Lord Nairne, to himself for life, and after his decease to his son-in-law, Lord william Murray, who assumed the surname of Nairne.