The monarch via The Royal Family verified Instagram and Twitter accounts shared pictures of Markle including one she took with the queen during their visit to Chester in 2018.
"Wishing the Duchess of Sussex a very happy birthday today!" The caption said.
The Duke and Duchess of Cambridge, Prince William and Kate Middleton also shared pictures of the Suits' actress on Twitter and said; "Wishing a happy 40th birthday to The Duchess of Sussex!"
Prince Harry's father and stepmother, Prince Charles and the Duchess of Cornwall also wished Meghan "a very happy 40th birthday," via their Clarence House accounts.
In what will precede a rocky relationship between the royal family and the couple, Markle alongside her husband, Prince Harry had stepped down from their positions as senior members of the royal family in March 2020 and moved to America.
Things got even more tense as the biracial mother of two gave an explosive interview with media personality, Oprah Winfrey in which she disclosed discrimination she faced as a member of the royal family
Joined by her husband, the couple disclosed several instances of what they perceived as racism, including a situation where there were conversations among unnamed royals about how dark their son, Archie's skin would be before he was born.
Meghan also revealed that continued attacks by the British media made her suicidal at some point while she had no defence from the royal family.
While the state of relationship between the couple and the royal family remains unclear, the birth of their new daughter Lilibeth-Diana in June seems to offer a fresh start.
Quite notable was Kate Middleton's comment when asked about her new niece during an engagement with US First Lady, Dr Jill Biden, at a school in Cornwall during the G7 Summit.
"I wish her all the very best. I can't wait to meet her. We haven't met yet. I hope that will be soon." She said.