The Honours as coronation regalia were first used together at the coronation of the nine-month-old Mary, Queen of Scots in 1543, and subsequently at the coronations of her infant son James VI (and I of England) at Stirling in 1567 and her grandson Charles I in 1633 at the Palace of Holyroodhouse.

Despite his success at the Battle of Dunbar in 1650 and his subsequent occupation of Edinburgh Castle, Oliver Cromwell failed to stop the coronation of Charles II in 1651 at Scone (the last coronation in Scotland). Determined to destroy the Scottish Crown Jewels, as he had disposed of the English regalia, Cromwell pursued the Honours to Dunnottar Castle but while the English laid siege the regalia were smuggled out of the castle by Mrs Granger, the wife of the minister of nearby Kinneff, and buried within the church.

The Honours remained hidden there until Charles II returned to the throne in 1660, when they were brought back to Edinburgh Castle. In the absence of a resident sovereign, the regalia were taken to sittings of the Parliament in Edinburgh to signify the sovereign's presence and his or her consent to the passing of each Act. The Honours were never again used to crown a sovereign.

In 1707 the Parliaments of Scotland and England were joined to form a single United Kingdom, whose Parliament met in London. A clause in the Treaty of Union decreed that the Honours should never leave Scotland ... and thus they were locked up in a chest in the Crown Room in Edinburgh Castle.

In 1818, the chest was opened in the presence of the Castle Governor and the author Sir Walter Scott. It was confirmed that the Honours were there, still in their linen wrappings.
In 1941 the Honours were hidden once again, buried in separate locations in the Castle as a precaution against possible German invasion.

The Honours were removed once from the Castle in 1953, to be taken to a National Service of Thanksgiving at the High Kirk of St Giles in Edinburgh, where they were formally presented to The Queen, who then returned them to their custodians.

Since 1819, the Honours (to which the Stone of Scone was added in 1996, after 700 years in Westminster Abbey) have been on public display in the Crown Room at Edinburgh Castle.