Upon John Maitland's return, through the influence of his brother, William Maitland, he received the offer of the position of Commendator of Kelso Abbey, which he shortly afterwards exchanged with Francis Stewart, later Earl of Bothwell, for the Priory of Coldingham. This transaction was ratified by Mary, Queen of Scots on 20 April 1567.
Upon the death of his father, he was appointed Keeper of the Privy Seal of Scotland, on 20 April 1567. He also supported Regent Moray, and sat in his parliaments in December 1567 and August 1568. On 2 June 1568 he was created a Senator of the College of Justice as an Ordinary Lord on the spiritual side. He retained the rich endowment of Coldingham until 1570.
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. At the end of 1570 he was denounced a rebel by the King's party, with his brothers William and Thomas, and they were all forfeited in the parliament which met in the Canongate, the so-called 'cropped parliament'.
John Maitland was deprived of all his offices and benefices, and took refuge in Edinburgh Castle. Upon its surrender on 29 May 1573 he was sent as a prisoner to Tantallon Castle in Haddingtonshire. After nine months' confinement there he was removed to Hugh, Lord Somerville's house of Cowthallie, under house arrest with bail at £10,000 Scots. In 1574/5 a Letter of Rehabilitation in his favour, as "Commendator of Coldingham", passed the Great Seal.
On 26 April 1581 he was reappointed Keeper of the Privy Seal of Scotland and returned to the Bench. He was shortly afterwards made a Privy Counsellor, and upon the dismissal of Abbot Pitcairn, appointed Secretary of Scotland on 18 May 1584. In the parliament which met on the 22nd of that month his doom of forfeiture was reduced, and he was restored to all the honours, heritages, and offices he had formerly possessed.
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.
Maitland was appointed Vice-Chancellor on 31 May 1586 and was also appointed Lord Chancellor of Scotland that year, following Earl of Arran's disgrace. The following year, 1587, saw him granted the barony of Stobo.
In 1589, a powerful combination, headed by the Earls of Huntly, Errol, and Bothwell, &c., was formed against Maitland. It was intended 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. The King and Maitland were not, however, at Holyroodhouse and the plot failed. Several other plots were formed against him shortly afterwards, but they were all defeated.
Maitland and Anne of Denmark
He was one of those who accompanied James VI on his matrimonial voyage to Norway and Denmark. Maitland was involved in financing and accounting for this journey. On 27 November, some of the ladies in waiting to Anne of Denmark asked him to join with Jens Nilssøn, Bishop of Oslo to intercede with James VI for the pardon of David Cunningham of Robertland. He had been welcomed at the Danish court after fleeing Scotland in the aftermath of the murder of the Earl of Eglinton in 1586. Maitland and the Danish ladies in waiting had an audience with the king in the Old Bishop's Palace and the laird of Robertland was pardoned.
On 15 December, James VI asked him to give the Danish counsellor Steno Brahe, brother of the astronomer Tycho Brahe, and the young king's lieutenant "Apill Gudlingstarre" or Axel Gyldenstierne gifts of silver plate from his cupboard, and Maitland was to keep the rest. The silver had been a gift to James VI from Queen Elizabeth, supplied by the London goldsmith Richard Martin.
Shortly after his return to Scotland, on 18 May 1590, he was made a Lord of Parliament with the title Lord Maitland of Thirlestane. 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." He consulted with Anne at Dunfermline Palace in July 1590 to ask her to appoint a household of ladies and gentlewomen to be about her. Sophie sent him a letter of thanks in June 1591, after hearing good reports from Wilhelm von der Wense. James had asked him to resolve issues over pay in the royal households in April 1591 after kitchen staff deserted their posts, and he reminded Maitland of promises he had made to Sophie, writing "Suppose we be not wealthy, let us be proud poor bodies".
James VI came to Thirlestane Castle on 15 February 1591 to celebrate the marriage of his niece to the laird of Lugton. Sir Robert Ker of Cessford had married his niece Margaret Maitland, and he was able to help Maitland into the favour of Anne of Denmark.
Anne of Denmark 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. Anne also believed she was the rightful owner of Musselburgh and Inveresk, lands belonging to Maitland, and these were transferred to her. In 1594 James VI appealed to her brother Christian IV of Denmark to ask her to take Maitland into her favour again.
In July 1595 Maitland wrote to the Earl of Essex, about their future "diligent intercourse of intelligence" involving the Scottish diplomat Richard Cockburn of Clerkington and Essex's secretary Anthony Bacon. Essex replied that he wrote only with the queen's knowledge, and they would be happy to receive letters from Maitland or Cockburn.
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. He was buried in a side chapel on the north side of St. Mary's, Haddington, where a splendid monument, with an epitaph, composed by King James VI, was erected to his memory.
Sir John Scot of Scotstarvet, writing in the seventeenth century, had this to say of the 1st Lord Maitland:
"Mr John Maitland, second brother to Secretary Maitland, after he had studied the laws in France, was preferred to be a Lord of Session by the said Earl of Arran's means, and thereafter became Chancellor. He was one of the Octavians [a name given to eight persons who managed affairs under king James VI], and was created Lord Thirlestane, and was an excellent Latin poet, as his verses inserted in Deliciae poetarum scotorum testify; and King James had such a respect to him, that he made the epitaph engraven on his tomb. Yet the conquest he made of the barony of Liddington [Lethington] from his brother's son, James Maitland, was not thought lawful nor conscientious."
- Anne (1589–1609) who married Robert Seton, 2nd Earl of Winton (but had no issue)
- John Maitland, 1st Earl of Lauderdale
- David Masson, Register of the Privy Council of Scotland: 1578-1585, vol. 3 (Edinburgh, 1880), p. 744: David Calderwood, iv, p. 366.
- National Records of Scotland, GD150.13789, GD40.1.739: Register of the Great Seal of Scotland, vol. 4, no. 2727.
- Miles Kerr-Peterson & Michael Pearce, 'James VI's English Subsidy and Danish Dowry Accounts, 1588-1596', Scottish History Society Miscellany XVI (Woodbridge, 2020), pp. 1-74.
- David Stevenson, Scotland's Last Royal Wedding (Edinburgh, 1997), pp. 94-5.
- David Masson, Register of the Privy Council, vol. 4 (Edinburgh, 1881), pp. 444-5: David Stevenson, Scotland's Last Royal Wedding (Edinburgh, 1997), pp. 39, 95.
- Calendar State Papers Scotland, vol. 10 (Edinburgh, 1936), pp. 160-162: Annie I. Cameron, Calendar State Papers Scotland: 1593-1595, vol. 11 (Edinburgh, 1936), p. 130.
- Calendar State Papers Scotland, vol. 10 (Edinburgh, 1936), p. 371: William Fraser, Memorials of the Earls of Haddington, vol. 2 (Edinburgh, 1889), p. 61.
- Calendar State Papers Scotland, vol. 10 (Edinburgh, 1936), p. 509.
- Calendar State Papers Scotland, vol. 10 (Edinburgh, 1936), p. 467.
- Thomas Thomson, Memoirs of his own Life (Edinburgh, 1827), p. 405.
- William Fraser, The Douglas Book, vol. 4 (Edinburgh, 1885), pp. 38-40.
- Annie I. Cameron, Warrender Papers, vol. 1 (Edinburgh, 1932), pp. 232-6, 237.
- HMC Mar & Kellie, vol. 2 (London, 1930), pp. 36-7.
- Calendar State Papers Scotland, vol. 12 (Edinburgh, 1952), pp. 18, 23, 28, 33, 34.
- Scot, John (1872). The Staggering State of the Scots Statesmen from 1550 to 1660. Edinburgh: Paterson. p. 43.
- An Historical Account of the Senators of the College of Justice of Scotland, by Sir David Dalrymple of Hailes, Bt., re-edited at Edinburgh in 1849, pps: 140–146 (who says he was "probably born in 1545").
- The Royal Families of England, Scotland, and Wales, with their Descendants, etc., by Messrs, John and John Bernard Burke, London, volume 1 (1848) pedigree XV, and volume 2 (1851), pedigree LXXXIV.
- History of the Priory of Coldingham, by William King Hunter of Stoneshiel, Edinburgh & London, 1858, pps: 72-3.
- Miscellanea Genealogica et Heraldica, edited by Joseph Jackson Howard, LL.D.,F.S.A., volume 2, London, 1876, p. 206.
- A satirical poem on the marriage of John Maitland and Jean Fleming by Hercules Rollock, Bridging the Continental Divide, University of Glasgow
- Miniature portrait of John Maitland of Thirlestane, National Portrait Gallery, London
- A portrait of John Maitland, painted over Mary Queen of Scots, Ham House, National Trust
- Portrait of John Maitland, John Scougal, Thirlestane Castle
| Keeper of the Privy Seal of Scotland
| Keeper of the Privy Seal of Scotland
Earl of Arran
| Lord Chancellor of Scotland
3rd Earl of Montrose
Archbishop of St Andrews
| Chancellor of the University of St Andrews
John Lindsay of Balcarres, Lord Menmuir