Following the Regent Moray's assassination, Maitland joined the Lords who met on the Queen's behalf at Linlithgow and shared in the dangers of the civil war which ensued.
He was shortly afterwards made a Privy Counsellor and, upon the dismissal of Robert Pitcairn, Abbot of Dunfermline, appointed Secretary of Scotland on 18 May 1584.
On 1 May 1585, plague came to Edinburgh and the king and councillors, including Maitland, went to Dirleton Castle, where their host James Stewart, Earl of Arran entertained them with a sumptuous banquet and a Robin Hood play.
The intention was to meet at Quarryholes, between Leith and Edinburgh, to march in a body to Holyroodhouse, make themselves master of the King's person, and put the Chancellor to death.
[6] Accounts of Maitland's expenses include the preparation of a ship, the James Royall of Ayr, hired from Robert Jameson, which was equipped with cannon by John Chisholm, painted, and supplied with new banners and red taffeta was stitched on the sails.
Anne of Denmark's mother Sophie of Mecklenburg-Güstrow had asked him to set up her daughter's household in Scotland and advise on matters of "honour and benefit."
[14] Sophie of Mecklenburg sent Maitland a letter of thanks in June 1591, after hearing good reports from Wilhelm von der Wense.
[15] James had asked him to resolve issues over pay in the royal households in April 1591 after kitchen staff deserted their posts, and discussed the subject of paying two departing members of the queen's household with either money or livery clothes,[16] and he reminded Maitland of promises he had made to Sophie, writing "Suppose we be not wealthy, let us be proud poor bodies".
[17][18][19] A cousin of James VI, Francis Stewart, 5th Earl of Bothwell, was implicated in the North Berwick Witch Trials on 15 April 1591 by the confession of Richie Graham.
[20] Anne of Denmark disapproved of the pursuit of the rebel Earl, and blamed Maitland for seeking the "wrack of the king's blood".
Anne of Denmark believed she was the rightful owner of Musselburgh and Inveresk, lands belonging to Maitland, which were properties of Abbey of Dunfermline south of the River Forth.
[23] She came to resent Maitland's powers and in January 1593 appealed for help against him and his wife, Jean Fleming, who she believed had slandered her and accused her of being complicit with the Earl of Bothwell.
[27] John Maitland died on 3 October 1595 at Thirlestane Castle, after a month's illness attended by the physician Dr Martin Schöner and the minister Robert Bruce.
Yet the conquest he made of the barony of Liddington [Lethington] from his brother's son, James Maitland, was not thought lawful nor conscientious.