While the royal family wished her a happy birthday on social media accounts, there were reports they would also have private video and phone calls with the monarch.
A spokesman for Harry and Meghan said that the couple were joined by their son Archie Mountbatten-Windsor during their personal call.
Harry, Meghan and Archie are living in Los Angeles, as they start a new chapter of their lives.
Harry and Meghan have been seen delivering food parcels to those in need through Project Angel Food, a charity in California.
The duchess will also be preparing for a court battle which begins on Friday, as she takes Associated Newspapers to court.
The queen, meanwhile, has been in isolation in Windsor, England, where she was joined by her husband Philip in March.
She asked that the usual celebrations of gun salutes not happen this year, and councils were told not to worry about flying the flag for the monarch’s birthday.
The queen’s official birthday events are also under review, with Trooping the Colour confirmed as not going ahead in its usual way this year.
Other members of the family shared their messages to the queen on social media, with Prince William and Kate Middleton posting a picture of them with her at the Chelsea Flower Show.
Prince Charles shared a series of images of the queen over the years, including one of her as a new mother with him as a baby.
But because Harry and Meghan can no longer use the word “royal” in any of their branding, they have had to mothball their popular Instagram account, which was called SussexRoyal. Although they have confirmed their new organization will be called Archewell, no official social media accounts have yet come to light.
Earlier on Tuesday, the royal family shared private footage from the royal collection, showing the queen as a child with her sister Margaret.
Last week, William revealed the royal family is making use of technology to keep in touch, which led to suggestions on whether there would be some Zoom calls made on Her Majesty’s birthday.
William told the BBC: “As you can imagine, the younger generation are a little bit more tech-savvy. But only just.
“I think we’re getting there now, the family are getting a little bit more used to being able to contact each other and pressing the right buttons and not dropping the computer halfway through.”
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