The note was nestled alongside a wreath of white blooms including lilies, roses, freesia and sweet peas, placed on top of Prince Philip’s coffin.
They were chosen by the Queen and included a handwritten card written by his wife of 73 years. Edged in black, the note poignantly said: ‘In loving memory’.
What was written below was hidden in the flowers but some reports have suggested the Queen signed it off as ‘Lilibet.’
It is the nickname she was given as a child and is used by her closest family members.
The Queen signed ‘Lilibet’ on the flowers at her mother’s funeral in 2002.
During the service today, the monarch wiped away tears and was forced to mourn alone away from her family in St George’s Chapel.
The Queen left a personal, hand-written message to Prince Philip at his funeral service today. but the content of the note is not known
Her Majesty looked grief-stricken and bowed her head in reverence as she accompanied her beloved Philip’s coffin on its final journey while their eldest son Prince Charles cried as he walked behind the casket into church followed by other devastated royals.
The Duke of Edinburgh’s coffin was covered in his personal standard and carried his sword, naval cap and a wreath of flowers as pallbearers placed him on to his extraordinary self-designed green Land Rover Defender hearse in the castle packed quadrangle packed with hundreds of armed personnel.
After the eight minute procession and the 50-minute service, his coffin was lowered into the Royal Vault.
A lament was played by a lone piper of the Royal Regiment of Scotland and the Last Post was then sounded by buglers of Philip’s beloved Royal Marines who then played Action Stations at the specific request of The Duke of Edinburgh.
Justin Welby, the Archbishop of Canterbury, pronounced the Blessing before the 30 royal mourners silently filed out of the church into cars to take them the short journey back to castle.
Harry and William decided to walk back with Kate, the Duchess of Cambridge, and were seen smiling speaking animatedly as they were reunited for the first time in a year where their relationship became fractured.
The emotional Queen had arrived at the funeral as the national anthem played and the royal Bentley stopped next to her beloved husband’s coffin, where she poignantly paused for a moment of reflection as cannons fired and bells tolled in remembrance of the duke.
Her Majesty was then driven to St George’s Chapel with a lady in waiting Susan Hussey, before being sat alone at the front of the church where she stood and bowed her head during the national minute’s silence. She looked at the coffin throughout the poignant service, where her children and grandchildren were on the verge of tears.
The couple, pictured together on their Diamond Wedding Anniversary in November 2007
Following behind the coffin was the royal procession, led by Philip’s children Prince Charles, Princess Anne, Prince Andrew and Prince Edward. The grandchildren, including Prince William and Prince Harry, followed but the feuding brothers were separated by their cousin Peter Phillips, viewed as a ‘peacemaker’ between the two.
The Duke of Cambridge entered the chapel one place ahead of his younger brother, as the mourners filed into the historic gothic building without saying anything to each other. But they later spoke as they walked back to the castle, with Kate taking a step back to let them spend time alone.
The Queen had decided that no royals should wear military uniform after Prince Andrew demanded to dress as an Admiral and Prince Harry was stripped of his titles. They were allowed to wear their medals, however.
As well as the monarch’s own private message, a handwritten card for the Duke was also left by Meghan Markle.
The Duchess of Sussex – who is around six-months pregnant with Prince Harry’s second child – was advised not to make the 10-hour flight to Britain for the funeral by her physician.
Instead, she watched the ceremony on television from her and Harry’s £11million mansion in California while her husband was in attendance.
A wreath from the couple was earlier left in St George’s Chapel, Windsor, to mark their respects, sources told PA news agency.
Meghan and Harry personally chose the locally-sourced flowers for their tribute – including Acanthus mollis (Bear’s breeches), the national flower of Greece, to represent Philip’s heritage, and Eryngium (sea holly), to represent the Royal Marines.
The wreath also features campanula for gratitude and everlasting love, rosemary to signify remembrance, lavender for devotion, and roses in honour of June being Philip’s birth month.