Her Majesty was forced to sit alone in St George’s Chapel as she bid farewell to her husband of 73 years.
She was joined by 29 other guests at the socially distanced ceremony at Windsor Castle on Saturday.
A total of 13.6 million people watched the moving service, which was broadcast live on the BBC.
What viewers didn’t know is that the Queen made a number of private tributes to the duke.
Here we take a look how.
Watch: The Queen Left Sweet Note — With a Nickname — on Prince Philip's Casket
Hidden photo and Philip’s handkerchief
The Queen is said to have brought a photo of herself and her husband with her to the service.
An insider told The Sun that the monarch had put a picture of herself and Philip, taken during their time in Malta, inside her handbag.
The source said she also had one of her husband’s handkerchiefs with her.
On top of Philip’s coffin, alongside the duke’s Admiral of the Fleet naval cap and sword, was a handwritten card reading "in loving memory".
The signature on the card was tucked out of sight but a source told People magazine that it said "Lilibet".
The Queen was given the nickname by her father George VI and it was adopted by her husband, who is thought to be the only other person to call her by that name.
The Queen picked out the flowers for the duke’s funeral herself.
For the wreath on top of his coffin she chose white lilies, small white roses, white freesia, white sweet peas and jasmine.
Guests were given a moment of privacy to say goodbye to the duke before his coffin was lowered into the Royal Vault by electric motor.
Just before the coffin disappeared the cameras cut away from the Queen to the piper, the buglers and trumpeters placed in the Nave.
The last tribute
The Queen picked a favourite picture of Prince Philip as her final tribute to him.
The Royal Family Twitter account shared an image of the Duke tipping his hat and walking away after the funeral finished.
The tweet read: “In loving memory of His Royal Highness The Prince Philip, Duke of Edinburgh. 1921-2021.”
Watch: The wonderful life of Prince Philip, The Duke of Edinburgh