As the hearse made its way from Aberdeenshire to the Palace of Holyroodhouse, where her body will spend the night, mourners lined the streets.
The next day, Monday, her casket will remain in vigil in Edinburgh's St. Giles' Cathedral before traveling to London in preparation for her funeral on Monday, September 19.
In the UK, crowds have assembled to hear King Charles III proclaimed.
As Charles travels to Scotland on Monday to accompany his mother's coffin to the church in the Scottish capital, he will be joined by members of the Royal Family.
Around 10:00 BST, the Queen's cortege departed from Balmoral and made its journey to Edinburgh, passing through Aberdeen and Dundee among other villages and towns.
Six hours later, as it passed through the heart of Edinburgh, there was a brief moment of stillness before the assembled audience began to applaud.
The Princess Royal, Princess Anne, and her husband, Vice Admiral Sir Tim Laurence, made the 175-mile trip in the cortege's second automobile.
As her mother's casket was brought into Holyroodhouse, the monarch's formal residence in Scotland, to rest in the throne room, she curtsied.
Along with the royal servants, the Duke of York and the Duke and Duchess of Wessex, who were present to receive the coffin, also bowed and curtsied, respectively.
Up until the Queen's funeral on Monday, the nation is in a state of mourning.
Following her passing on Thursday at the age of 96, a number of constitutional and ceremonial activities will be held over the following days.
Before she departed for the last time from her beloved private Scottish home, Balmoral, six gamekeepers from her Balmoral estate loaded the Queen's oak casket into a hearse earlier on in the voyage.
Some of the Queen's favorite flowers, all picked from the estate (white heather, dahlias and sweet peas, phlox and pine fir), were included in the wreath atop the coffin.
The closest village to Balmoral was Ballater, Aberdeenshire, where the cortege arrived.
The public is welcome to pay their respects while the casket is kept at St. Giles' Cathedral under 24-hour vigil.
The cathedral will host a service that evening.
Princess Anne will fly with her mother's coffin from Edinburgh Airport back to Buckingham Palace the next day, via RAF Northolt in north-west London.
Thousands of people gathered in Windsor at the same time to honor the Queen.
While floral tributes and cards were still being left outside the castle walls, roads were closed.
Thousands more flower tributes were also left in Green Park, next to Buckingham Palace, in honor of the Queen.