[2] During travels in France and Switzerland Lindsay imbibed Reformation principles, and he was one of the twelve original ministers nominated in July 1560 to the "chief places in Scotland", the town assigned him being Leith.
The intercession having failed, Lindsay, at Kirkcaldy's special request, attended him on the scaffold, and thus, according to Calderwood, became witness of the literal fulfilment of the doom pronounced by Knox.
On the arrival shortly afterwards of Esmé Stuart, the secret catholic emissary from France, Lindsay, at the king's request was, on account of his knowledge of French, appointed by the kirk to attend on him with a view to his conversion to protestantism.
On this account he was in May 1584 selected by the ministers in and around Edinburgh to induce the king to delay his assent, until a meeting of the assembly, to certain acts circumscribing the authority of the kirk; but as he entered the palace gate he was apprehended and lodged in Blackness Castle.
As chaplain of the king Lindsay accompanied him in October 1589 when he set sail for Norway to bring home his bride, Anne of Denmark.
Lindsay came to Edinburgh from Falkland Palace in 1600 in order to assure the clergy of the truth of the official version of the Gowrie House conspiracy of 5 August 1600.
[9] Soon afterwards he received a special mark of royal favour by his crown provision on 5 November 1600, in accordance with the act for the establishment of a modified episcopacy, to the bishopric of Ross.
"He was", says the same authority, "of a placable nature, and greatly favoured of the king, to whom he performed diverse good services, especially in the troubles he had with the church: a man universally beloved and well-esteemed of by all wise men".