On 27 March 1530, Elizabeth married George Gordon, 4th Earl of Huntly, the wealthiest and most powerful landowner in the Scottish Highlands, whose estates approached those of an independent monarch. He was also the leading Catholic magnate in Scotland. Her brother promised to give Elizabeth five thousands merks as a tocher. Upon her marriage, Elizabeth became the Countess of Huntly. The Huntlys' chief residence was Strathbogie Castle in the Scottish Highlands. The Earl became Lord Chancellor of Scotland in 1546 following the death of David Beaton, Archbishop of St. Andrews. He was taken prisoner at the battle of Pinkie on 10 September 1547 and Elizabeth came with him to Berwick-upon-Tweed, returning to Scotland at the end of the month. He and Elizabeth together had a total of 12 children:
Lady Margaret Gordon, married John Forbes, 8th Lord Forbes, by whom she had issue.
Lady Jean Gordon, married firstly on 24 February 1566, James Hepburn, 4th Earl of Bothwell, whom she divorced on 3 May 1567; secondly on 13 December 1573, Alexander Gordon, 12th Earl of Sutherland, by whom she had issue; and thirdly in December 1599 Alexander Ogilvy of Boyne.
Elizabeth was described as having made all the decisions for her husband, and often "turned to the aid of her familiars and witches when inspiration from any other source was lacking". She was better educated and her writing was superior to that of the Earl. She also was surrounded by a large and splendid train of personal attendants. On 23 August 1550, she ordered the execution of William MacIntosh, 15th Laird MacIntosh for having committed treason against Huntly who was accompanying the Scottish RegentMarie of Guise to her native France. In 1562, after her husband's title of Earl of Moray was taken from him and granted to Lord James Stewart, the illegitimate half-brother of Mary, Queen of Scots and husband of Elizabeth's niece Lady Agnes Keith the Earl of Huntly rebelled and raised a force of his own retainers against Queen Mary. Elizabeth encouraged her husband in his rebellion, and persuaded him to attack the queen's troops at Aberdeen and there apprehend Queen Mary. with the purpose of forcing her into marriage with their son, Sir John. On 22 October, at the Battle of Corrichie, Huntly and his men were defeated by Queen Mary's army led by James Stewart, Earl of Moray. Huntly died of apoplexy on the battlefield, while Elizabeth's sons John and Adam, themselves having actively participated in the rebellion and battle, were captured and shortly afterwards on 2 November, Sir John was executed by the orders of Queen Mary for treason. The life of seventeen-year-old Adam was spared as was that of George, Lord Gordon who had denied the queen entrance to the castle of Inverness where he held the post of sheriff; George, although pardoned, was nonetheless ordered to Dunbar Castle where he remained in custody until 1565 when his dignities were nominally restored to him. In 1563, the year following the Battle of Corrichie, Huntly's title and possessions were forfeited to the crown at a macabre session of Parliament with Queen Mary in attendance, in which his embalmed corpse was set up for all to see, and was pronounced guilty of treason and the sentence of passed upon it. Strathbogie Castle was duly stripped of its furnishings and these were sent to the queen's palace of Holyrood and to the Earl of Moray's new castle of Darnaway. Among the Huntlys' confiscated belongings were elaborate tapestries, velvet-covered beds, hung with fringes of gold and silverwork, figures of animals, and vessels of gilded and coloured glass. Later, as a token of the queen's clemency towards the Huntlys, Elizabeth and her second eldest daughter, Jean were given positions at the royal court. On 24 February 1566, Jean became the first wife of James Hepburn, Earl of Bothwell who, following his divorce from Jean in 1567, would marry as her third husband, Mary, Queen of Scots. In March 1566, Elizabeth, who had by that time become a loyal adherent of Queen Mary, spent the night tending the queen, who was in her sixth month of pregnancy, at Holyrood Palace following the murder of David Rizzio. She devised various plans for Mary's escape which the latter rejected as having been impracticable. She finally managed to smuggle a letter to her son George, who also had become Mary's partisan, ordering him to stand by at Seton with a party of nobles to aid the queen on her journey to Dunbar Castle after she successfully escaped from the palace. Elizabeth Gordon died on an unknown date.
