Bystanders at the foot of Arthur’s Seat watched as the monarch’s helicopter landed in parkland – close to the rear entrance to her official residence at the Palace of Holyrood.
One onlooker told of their surprise to see her emerge from the enormous red chopper.
"She hopped out of it and got into a smart car and was escorted off,” they said.
The Queen is currently visiting Scotland for the annual Holyrood Week with other members of the royal family - her first trip since the death of her husband, the Duke of Edinburgh.
The sighting comes after the Queen met with First Minister Nicola Sturgeon on Tuesday morning.
During the First Minister's visit to the Royal residence on Monday, she was heard saying to the Queen: “It’s very nice to be back.”
The Queen said: “We are still rather distanced I’m afraid” as the Scottish First Minister replied: “that’s very wise”.
On Monday, the Queen was introduced to Scotland’s “other national drink”, Irn-Bru at the Cumbernauld factory.
Along with the Duke of Cambridge, who is known as the Earl of Strathearn in Scotland, she was present for the Ceremony of the Keys on the forecourt of the Edinburgh palace.
The Ceremony of the Keys saw the monarch handed the keys of the city and welcomed to "your ancient and hereditary kingdom of Scotland" by Edinburgh Lord Provost Frank Ross.