February 11, 2020 | 12:25pm

Queen Elizabeth’s “favorite” grandson Peter Phillips will split from his wife Autumn Kelly — leaving the monarch “upset” and sparking concerns that the bombshell “Megxit” announcement may have influenced the decision, according to new reports.

Peter, 42, and Autumn, 41 — both of whom are not considered “working royals” and hold jobs outside the royal family — announced they have “jointly” agreed to separate in a Tuesday statement. Peter is the son of Princess Anne and her first husband Captain Mark Phillips.

“They had reached the conclusion that this was the best course of action for their two children and ongoing friendship,” said the statement, issued to Town & Country.

“The decision to divorce and share custody came about after many months of discussions and although sad, is an amicable one. The couple’s first priority will remain the continued well-being and upbringing of their wonderful daughters Savannah (9) and Isla (7).”

Peter and Autumn will co-parent the girls and remain in Gloucestershire, “where they have been settled for a number of years,” according to the statement.

The news comes in the midst of a turbulent time for the Royal Family — already battered with the fallout from Prince Andrew’s car crash interview on his relationship with Jeffrey Epstein, as well as Prince Harry and Meghan Markle’s decisions to step down as senior royals.

“The Queen must wonder what she has done to deserve this,” a senior royal source told The Sun. “Peter Phillips has always been a favorite of hers and Prince Philip and she will be crestfallen by this, especially on top of all the other bad news. It makes you wonder what’s going to happen next.”

Close friends have suggested that Harry and Meghan’s sudden move from the UK to Canada may have influenced Autumn — who is initially from the Great White North.

“What worries some of us is that Autumn may want to go back to Canada,” one friend told The Sun. “Maybe she has been influenced by Harry and Meghan’s departure. Perhaps she thought, if that can happen, then I can leave as well? That might be unfair on her but you have to consider it.”

Meanwhile, a friend of Peter told the outlet he is “absolutely devastated by this and just didn’t see it coming.”

“He thought he was happily married and had the perfect family with two lovely daughters,” the friend said. “But he is now in total shock.”

“Autumn is a wonderful wife and mother and a very intelligent woman but she’s been telling her friends for some time that there were issues,” the pal continued. “She is a favorite of the Queen and I’m sure Her Majesty will be very upset by this as well. It’s the last thing she needs after all her recent troubles and you get the feeling that the Royal Family is falling apart a little bit.”

Peter and Autumn married at St. George’s Chapel in Windsor in 2008.