After the assassination of Regent Moray in January 1570, Lord Lindsay assisted in carrying the corpse of the Regent Moray at his funeral at St Giles, Edinburgh. Subsequently, during the Marian civil war, he supported the king's party. On 16 June 1571 the forces under him and Morton slew Gavin Hamilton, commendator of Kilwinning, and took Lord Home and others prisoners. On the last day of the same month, he also intercepted at Wemyss a quantity of gold sent by order of Queen Mary with John Chisholm for the defenders of the castle, from her dowry out of France. Shortly afterwards he was taken prisoner, but on 12 July he purchased his liberty. A few months later a party of horsemen from Edinburgh went to his estate of the Byres and seized a large number of his cattle, but on the following day, Lindsay, in a victorious skirmish with the enemy in the High Street of Edinburgh, took Lord Seton prisoner.