Jean Fleming shared in her husband's work as Chancellor of Scotland. An English visitor at the Scottish court, Thomas Fowler, wrote that she was "a wise woman and half chancellor when he is at home." The goldsmith and royal financier Thomas Foulis made two accounts of money for the mint received from "Lady Thirlestane." The first of the "Lady Chancellaris" accounts commenced on 20 June 1589, and the second began on 1 August 1590. Fleming received an amethyst ring and large sums of money, perhaps connected with the reception of the royal bride. In February 1590 she was pregnant with her daughter Anne, as a newsletter noted, "The Lady Chanceller feeles the motion of a barne within her weam." In May 1590 she greeted the new queen of Scotland Anne of Denmark at the Shore of Leith, with the Countess of Mar, Lady Seton, Lady Boyne, and Lady Dudhope. She managed to make an enemy of Anna of Denmark by remarking in her hearing of Anne's supposed relationship with Francis Stewart, 5th Earl of Bothwell, who had been imprisoned for witchcraft in connections with events around the marriage of Anne and James, and whose trajectory from this point forwards was escape, exile, forfeiture and death. The queen wrote a letter mentioning her accusation that she was complicit with the Earl of Bothwell. In September and October 1592 Maitland and his wife were at Greenlaw with the Provost of Lincluden and at Kenmure and Drumlanrig with John Gordon of Lochinvar. Fleming then visited the court. The English ambassador Robert Bowes mentioned the queen's antipathy towards her in September 1593. She was again in the queen's favour by February 1595.
Countess of Cassilis
On Maitland's death on 3 October 1595 Jean was left a rich widow, and quickly married John Kennedy, 5th Earl of Cassilis, some 22-years her junior, becoming Countess of Cassillis. The age disparity aroused considerable scornful comment in the Scottish court, but Jean's wealth ensured the continued status of the couple. It was said, "she was past bairns bearing, and he was a young man not past 23 years." Kennedy was offered a post as Treasurer in 1599, but declined, fearing the cost of the appointment in terms of anticipated loans to a needy James VI. On 22 February 1600 Fleming and Cassilis hosted James VI at Thirlestane Castle. In 1602 she was contrasted with the Catholic Lady Livingstone as "a lady without all religion". As part of the marriage contract of her daughter Anna Maitland and the Master of Winton, Jean Fleming rebuilt Winton Castle for the couple, and the Earl of Winton owed her 2,000 merks for this. Kennedy was imprisoned twice in 1604 for doing violence to Jean, the first incident involving him dragging her from court before witnesses. King James advised the Privy Council of Scotland to protect her financial interests from her husband. During this period it was alleged that Hector Ferguson of Letterpin had ambushed Jean Fleming and servants between the Inch of Galloway and Maybole, and chased her to Maybole Castle. Jean Fleming died in Edinburgh after a period of illness on 23 June 1609 and is buried in St Mary's Collegiate Church, Haddington.
