The monarch, 95, had been staying at her Scottish residence since 23 July and she was visited by family members over the summer, including the Duke and Duchess of Cambridge, and Princess Eugenie, Jack Brooksbank, and their baby son August.
WATCH: The Queen receives sweet card from schoolchildren in Balmoral
Her Majesty has already begun her busy autumn schedule of public engagements. On Friday, she was joined by the Prince of Wales as they marked the start of the official tree planting season for the Queen's Green Canopy (QGC).
The Queen was then accompanied by Prince Charles and the Duchess of Cornwall as she opened the sixth session of the Scottish Parliament on Saturday.
During her address, the monarch spoke about her late husband, who passed away in April: "I have spoken before of my deep and abiding affection for this wonderful country, and of the many happy memories Prince Philip and I always held of our time here.
"It is often said that it is the people that make a place, and there are few places where this is truer than in Scotland, as we have seen in recent times."
The Queen was joined by Charles and Camilla at the opening of the Scottish Parliament
On Tuesday, the Queen will be accompanied by her youngest son, the Earl of Wessex, at Buckingham Palace, as they launch the Queen's Baton Relay for the Birmingham 2022 Commonwealth Games.
For the past 18 months, Her Majesty has resided mostly at Windsor Castle.
While many of the Queen's engagements took place via video or telephone calls during the last lockdown, she began carrying out in-person engagements again from March.
On 12 October, she will be joined by her daughter, the Princess Royal, at a Service of Thanksgiving at Westminster Abbey to mark the centenary of the Royal British Legion.
Her Majesty will also host a reception at Windsor Castle to mark the Global Investment Summit on 19 October.
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