Thousands of members of the public moved solemnly past the oak coffin through the night as it stood on public view for 24 hours at St Giles’ Cathedral in Edinburgh.
Charles, on his Operation Spring Tide tour around the UK with the Queen Consort, will leave Scotland and head to Belfast before returning to London in the evening.
Members of the public are already queueing for the Queen’s lying in state at Westminster Hall, which opens on Wednesday, and thousands are still placing floral tributes in Green Park.
Mourners have been asked by Royal Parks not leave marmalade sandwiches – a nod to the Queen’s comedy sketch with Paddington Bear – for fear of a negative effect on wildlife.
At 6pm, the Queen will depart Scotland for the last time.
Her coffin will be flown from Edinburgh Airport to London on an RAF Globemaster C-17 flight, accompanied by her daughter the Princess Royal.
The King will be joined by Camilla as he receives his mother’s coffin at Buckingham Palace, where she spent so many of her decades as sovereign.
The Prince and Princess of Wales will also be at the Palace.
A guard of honour formed of three officers and 96 soldiers from The King’s Guard will be mounted in the Quadrangle.
Military commands, usually shouted, will be given as quietly as possible in honour of the solemn occasion.
The coffin will be carried by a bearer party to the Bow Room where a sovereign’s piper will play a lament.
It will remain in the Bow Room overnight before a procession on Wednesday to Westminster Hall for the start of the lying in state.
The King’s visit to Northern Ireland earlier in the day comes ahead of a trip to Wales later in the week.
After touching down in Belfast, Charles and Camilla are to travel to Hillsborough Castle in Co Down, the royal residence in Northern Ireland, for several engagements.
They will hold a private audience with the new Northern Ireland Secretary Chris Heaton-Harris, as well as meeting representatives of political parties in the region.
The couple will then receive a message of condolence on behalf of the people of Northern Ireland from the speaker of the Stormont Assembly Alex Maskey.
They will then go to a reception at the castle, hosted by Mr Heaton-Harris, which some members of the public will also attend.
Charles and Camilla will then travel to St Anne’s Cathedral in Belfast where they will attend a service of reflection for the life of the Queen.
The new monarch will also meet leaders from all the major faiths in Northern Ireland.
Before leaving, Charles and Camilla will undertake a walkabout at Writers’ Square.
Although the square will be closed to the public, people are being invited to line the route to Hillsborough Castle and the route to the cathedral.
The royal couple will travel along Main Street and Lisburn Street in Hillsborough before heading to Belfast along Wellington Place, Donegall Square North, Chichester Street and Victoria Street.
Irish President Michael D Higgins and his wife Sabina, Taoiseach Micheal Martin and Foreign Affairs Minister Simon Coveney are due to attend the memorial service at St Anne’s Cathedral.
Both Houses of Parliament gathered at Westminster Hall in London on Monday to express their condolences to the new monarch, and Charles promised “faithfully to follow” the example set by his mother.
Later, the King led the royal family in a procession behind the Queen’s coffin in Edinburgh as it was taken from the Palace of Holyroodhouse to St Giles’ Cathedral.