An active Protestant, Lindsay wrote to Elizabeth I of England in favour of the Puritan preacher John Udall.
In 1592 the printer Robert Waldegrave dedicated an edition of Dudley Fenner's Certain Godly and Learned Treatises to him.
On 17 November 1592 Margaret Douglas, the heavily pregnant wife of the rebel Earl of Bothwell kneeled on the street before James VI as he was going to Edinburgh Castle, and after Lord Home and Lord Lindsay spoke in her favour she was allowed to kiss the king's hand, who then spoke harshly of her and her husband.
[4] On 17 December 1596, he was involved in a riot at the Tolbooth Church in Edinburgh against the Octavians which was declared treason.
At first Anne of Denmark hoped to use the profit of his goods as a dowry for Jean Stewart, one of her ladies-in-waiting.