In 1057 she arrived at the English court of Edward the Confessor (his great-niece). Ten years later she was in exile after William defeated Harold at the Battle of Hastings. She fled to Scotland where she was married against her wishes to King Malcolm to whom she bore six sons and two daughters. Her unlearned and boorish husband grew daily more graceful and Christian under the queen's graceful influence.

Margaret also built what was later to be known as St Margaret's Chapel, situated on the highest part of Edinburgh Castle.

In her position as queen, all Margaret's great influence was thrown into the cause of religion and piety. A synod was held, and among the special reforms instituted the most important were the regulation of the Lenten fast, observance of the Easter communion, and the removal of certain abuses concerning marriage within the prohibited degrees. Her private life was given up to constant prayer and practices of piety. She founded several churches, including the Abbey of Dunfermline, built to enshrine her greatest treasure, a relic of the true Cross. Her book of the Gospels, richly adorned with jewels, which one day dropped into a river and was according to legend miraculously recovered, is now in the Bodleian library at Oxford. She foretold the day of her death, which took place at Edinburgh on 16 Nov., 1093, her body being buried before the high altar at Dunfermline.

In 1250 Margaret was canonized by Innocent IV, and her relics were translated on 19 June, 1259, to a new shrine, the base of which is still visible beyond the modern east wall of the restored church. At the Reformation her head passed into the possession of Mary Queen of Scots, and later was secured by the Jesuits at Douai, where it is believed to have perished during the French Revolution. According to George Conn, "De duplici statu religionis apud Scots" (Rome, 1628), the rest of the relics, together with those of Malcolm, were acquired by Philip II of Spain, and placed in two urns in the Escorial. When, however, Bishop Gillies of Edinburgh applied through Pius IX for their restoration to Scotland, they could not be found.

The chief authority for Margaret's life is the contemporary biography printed in "Acta SS.", II, June, 320. Its authorship has been ascribed to Turgot, the saint's confessor, a monk of Durham and later Archbishop of St. Andrews, and also to Theodoric, a somewhat obscure monk; but in spite of much controversy the point remains quite unsettled. The feast of St. Margaret is now observed by the whole Church on 10 June.