The Gilmours left Craigmillar in the 18th century for a more modern residence, nearby Inch House, and the castle fell into ruin.

Before she left on 7 December 1566, a pact known as the "Craigmillar Bond" was made, with or without her knowledge, to dispose of her husband Henry Stuart, Lord Darnley.

In a further grant of 1374, King Robert II gave the remaining lands of Craigmillar to Sir Simon de Preston, Sheriff of Midlothian.

[4] The courtyard wall was probably added by Sir William Preston (d. 1453), who had travelled in France, and drew on continental inspiration for his new work.

[5] He also brought back the arm of Saint Giles, which he presented to the High Kirk of Edinburgh, where the Preston Aisle is named for him.

In 1511 Craigmillar was erected into a barony, and the outer courtyard was built around this time, possibly by another Simon Preston (d.1520), Member of Parliament for Edinburgh in 1487, who had succeeded in 1478.

His French guardian De la Bastie had new locks made for his chamber and the two iron gates, and a stable was built for the king's mule.

[9] During the so-called Rough Wooing of Henry VIII of England, the English attempted to impose, by military force, a marriage between Edward, Prince of Wales, and the young Mary, Queen of Scots.

[5][11] Preston served as Lord Provost of Edinburgh for several years, and was a loyal supporter of Queen Mary, who appointed him to her Privy Council.

[13] She stayed from 20 November to 7 December 1566, still in poor health following a serious illness in October, and, according to Philibert du Croc, suffering from depression.

[14] She gave an audience to a diplomat from Savoy, Jean, Count de Brienne, who had arrived for the baptism of Prince James.

[15] Mary is traditionally said to have slept in the small former kitchen within the tower house, although it is more likely that she occupied larger accommodation in the relatively new east range.

[16] Several of her noblemen were with her at Craigmillar in November 1566, and suggested to her that her unpopular husband, Henry Stuart, Lord Darnley, could be removed, either by divorce or by other means.

[17] An agreement, the "Craigmillar Bond", was signed by Mary's Secretary of State William Maitland of Lethington, and several nobles including the earls of Bothwell, Argyll and Huntly.

[18] It was initially intended that Darnley would lodge at Craigmillar when he returned to Edinburgh, although he opted to stay at Kirk o' Field in the town, where he was murdered on 10 February 1567.

[12] During the Marian Civil War, Captain Melville and two of his soldiers, who fought for Mary's cause, were killed in the grounds of the castle on 2 June 1571 when a barrel of gunpowder exploded.

[5] In September 1589 James had been at Seton Palace expecting the arrival of Anne of Denmark, and came to Craigmillar still waiting for news of his bride, "as a kind lover spends the time in sighing".

[23] In 1591, Agnes Sampson was accused of placing a charmed wax image in a dovecote at Craigmillar to help her friend Barbara Napier.

His son sold the castle out of the family, and it was bought by Sir John Gilmour (d.1671) in 1660,[5] who purchased the neighbouring estate of The Inch at the same time.

A stair leads up from the entrance to a guard room in the jamb, which would probably have had "murder holes" through which missiles could be dropped on any attackers who gained entry.

[16] The exterior of the castle formerly had two timber balconies, or viewing platforms, one overlooking the gardens to the south, and one looking east across the Lothian countryside.

The original east range, contemporary with the courtyard wall, was rebuilt in the 16th century and linked to the tower house by a new, broad spiral stair.

[37] South of the castle were informal gardens and orchards, with the bases of 16th-century viewing towers remaining at the corners of this drystone-walled enclosure.

The former fish pond, shaped like a letter P for Preston, is a nationally significant archaeological garden feature, due to its rarity.