Prince Harry is said to have told the Queen that he would accept dropping his royal titles during a personal phone call.
The Duke of Sussex, 36, spoke with Her Majesty early last month to make sure he was happy with his decision and his new life in the US, The Telegraph reports.
Following the call from Windsor Castle to the duke and wife Meghan's new £11million California mansion 5,500 miles away, the Queen, 94, asked courtiers to announce the couple would not be returning to royal duties.
Buckingham Palace revealed the Sussexes would be leaving their roles in January last year.
As part of their request for independence, the pair agreed to drop their HRH titles, no longer receive public funding and stop officially representing the Queen.
They also said they would £2.4m of taxpayer money for the refurbishment of Frogmore Cottage – their UK family home.
The couple and son Archie initially moved to Canada shortly after the announcement before buying their plush US pad in June.
Announcing their decision to leave the royals, The Queen released a statement, which stated following "many months of conversations and more recent discussions" she was "pleased that together we have found a constructive and supportive way forward for my grandson and his family".
"Harry, Meghan and Archie will always be much loved members of my family," the statement continued.
She also thanked them for their "dedicated work", adding that she was "particularly proud of how Meghan has so quickly become one of the family."
Prince Harry 'devastated' to lose military titles as 'best of both worlds' plan fails
Since moving Stateside, Harry and Meghan have secured multimillion-pound deals with Spotify and Netflix.
The Duchess has also become a property investor, while the couple have launched Archewell, a nonprofit foundation.
When the shock announcement was first revealed last year, the couple wanted to keep their royal patronages, including Harry's treasured honorary military titles and were believed to be considering a senior position in the Commonwealth.
But the "half-in-half-out option" was deemed "very difficult to pull off" by palace officials.
Royals are banned from pursuing private business ventures while representing the Queen.
What's more, Her Majesty denied the duke's call to lay a wreath on his behalf at the Cenotaph on Remembrance Sunday. Instead, the Sussexes staged a private ceremony in Los Angeles.
Formal discussions about the couple's future also included Harry's dad, the Prince of Wales, and brother the Duke of Cambridge.
Meghan Markle and Prince Harry 'hit the roof' when Queen revoked titles after Megxit
One source close to Prince Harry told the Telegraph: "The royal appointments and patronages were never in their gift.
"All they have done is express their commitment to them. There is no question that if it was up to them, they would keep them."
The Queen will have expressed sympathy for her grandson as she dealt this final blow.
Aware that his time in the Army was the making of him, she has witnessed him take that experience and use it to phenomenal effect, not least with the hugely successful Invictus Games.
But yesterday a palace source told the Telegraph: "The Queen made the position clear last January and nothing has changed.
"She told them, if you want to lead an independent life, then good luck to you but you can't do both. She has never wavered on that.
"At the same time, the Sussexes remain much-loved members of her family. They might live in the US, but they are not exiled in the US."
Harry and Meghan will be interviewed by chat show host Oprah Winfrey on US TV network CBS on March 7.
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