In November 1542, he was taken prisoner by the English at the Battle of Solway Moss, but released at a ransom of 1,000 marks, paid on 1 July 1548. During the Regency of the Earl of Arran he took messages from Mary of Guise to the English ambassador Ralph Sadler. He was also happy to receive English messengers at his home at Cumbernauld Castle in 1544.
Fleming's principal house was Boghall at Biggar, where he founded the collegiate church in 1545. The Tweedie family had already endowed a chaplain there in 1531 as part of the resolution of the feud.
- James Fleming, 4th Lord Fleming, who married Barbara Hamilton
- John Fleming, 5th Lord Fleming
- Joanna Fleming, who first married John Livingston, Master of Livingston and eldest son of Alexander Livingston, 5th Lord Livingston, who was killed at the Battle of Pinkie along with her father. Sometime after 24 May 1560, she married John Sandilands of Calder, who died in May 1567, with whom she had issue. Before November 1567, she married for the third time to David Craufurd of Kerse.
- Janet Fleming, who married Richard Brown, Younger of Hartree, who died after 23 September 1536. Their son and heir apparent was Andrew Brown of Hartree
- Agnes Fleming (died before 18 October 1597), who married before 1 October 1553, William Livingstone, 6th Lord Livingston, and had issue
- Margaret Fleming (died before 15 Mar 1586/7), who married Robert Graham, Lord Graham, who died at the Battle of Pinkie, and had issue, William Graham, 2nd Earl of Montrose. Sometime after 30 Jan 1548/9, she married Thomas Erskine, Master of Erskine, a son of John Erskine, 5th Lord Erskine. On 1 April 1557, she married for the third time to John Stewart, 4th Earl of Atholl.
- Mary Fleming, a Lady-in-Waiting to Mary Queen of Scots, who married Mary's secretary, William Maitland of Lethington. After his death, she married George Meldrum of Fyvie.
- Elizabeth Fleming (died after 1550), who married before 24 March 1540/1 William Crichton, 5th Lord Crichton of Sanquhar, and had issue including Robert Crichton, 6th Lord Crichton of Sanquhar
He also had illegitimate sons called John and William.
He died on 10 September 1547, aged 53, being slain at the Battle of Pinkie. His will included £50 owed to him by Mary of Guise, and in it he wished to be buried in his new church and his father's remains to be taken there from Boghall. Cumbernauld Castle went to his eldest son, James Fleming. His wife was to have Boghall excepting its artillery.
- Strickland, Agnes, Lives, vol. 2 (1851), 39-41: Sadler State Papers, vol.1, (1809), 134-5, Sadler to Henry VIII, 9 April 1543.
- Letters and Papers Henry VIII, vol. 19 part 1 (1903) no. 299 (3) & footnote.
- Cameron, Jamie, James V, Tuckwell (1998), p.103.
- "Archived copy". Archived from the original on 8 March 2012. Retrieved 31 October 2011.CS1 maint: archived copy as title (link)
- Miscellany of the Spalding Club, vol. 2 (1852) 296-315, text of church foundation charter (Latin) and will.
- The Complete Peerage of England, Scotland, Ireland, Great Britain, and the United Kingdom Extant, Extinct, or Dormant; first edition by George Edward Cokayne, Clarenceux King of Arms
|Peerage of Scotland|
| Lords Fleming
1524 – 1547