Prince Philip, 99, was pictured smiling and waving as he was driven out of the castle's gates.
In photographs published by The Sun, the couple were spotted boarding a plane at Aberdeen airport. The 94-year-old monarch looked elegant in a cream checked coat and a patterned head scarf as she stepped out of the car.
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The Queen and the Duke have been residing at Balmoral Castle since 4 August and have hosted family members during their traditional summer break.
Among their visitors were the Earl and Countess of Wessex and their children, Lady Louise Windsor and James, Viscount Severn, Princess Eugenie and her husband Jack Brooksbank, as well as the Duke and Duchess of Cambridge and their three children George, Charlotte and Louis.
The Duke waves to well wishers
Her Majesty and her husband are set to spend time privately together on the Sandringham Estate in Norfolk for the remainder of the month.
The Queen typically spends her winter break at her Sandringham estate, travelling up to Norfolk after the Christmas party for extended family members at Buckingham Palace in December.
The Queen and the Duke travelled to Sandringham on Wednesday
In a statement released by Buckingham Palace last week, a spokesperson added: "Subject to the finalisation of the autumn programme, Her Majesty's intention is to return to Windsor Castle in October and to resume the use of Buckingham Palace for selected audiences and engagements. These plans will be kept under review and will of course be subject to all relevant guidance and advice."
It is not yet known whether Prince Philip will remain on the Sandringham Estate when the Queen returns to Windsor, or whether he will join the monarch at the Berkshire castle where they spent lockdown.
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