Pope Innocent IV canonized St. Margaret in 1250 in recognition of her personal holiness, fidelity to the Roman Catholic Church, work for ecclesiastical reform, and charity. On 19 June 1250, after her canonisation, her remains were transferred to a chapel in the eastern apse of Dunfermline Abbey in Fife, Scotland. In 1693 Pope Innocent XII moved her feast day to 10 June in recognition of the birthdate of the son of James VII of Scotland and II of England. In the revision of the General Roman Calendar in 1969, 16 November became free and the Church transferred her feast day to 16 November, the date of her death, on which it always had been observed in Scotland. However, some traditionalist Catholics continue to celebrate her feast day on 10 June.

She is also venerated as a saint in the Anglican Church.

Institutions bearing her name

Several churches throughout the world are dedicated in honour of St Margaret. One of the oldest is St Margaret's Chapel in Edinburgh Castle in Edinburgh, Scotland, which her son King David I founded. The Chapel was long thought to have been the oratory of Margaret herself, but is now thought to have been established in the 12th century. The oldest edifice in Edinburgh, it was restored in the 19th century and refurbished in the 1990s. Numerous other institutions are named for her as well.