All looked happy and relaxed as they followed the Duke of Edinburgh, at the traditional Christmas day church service.
The Queen praised Manchester, hit by a suicide bomber in May, and London, which endured attacks on Parliament, London Bridge and other landmarks.
"This Christmas, I think of London and Manchester, whose powerful identities shone through over the past 12 months in the face of appalling attacks", she said in the speech. This was also one of the reasons why Ivanka Trump's well-wishes to Markle and Prince Harry after they announced their engagement were criticized by many.
"I describe that hospital visit as a "privilege" because the patients I met were an example to us all, showing extraordinary bravery and resilience", she said. The little royals did not attend the morning service, however.
The Queen and Philip are spending the holidays at Elizabeth's country estate in Sandringham, 175 kilometres north of London.
The Queen positioned an engagement photo of Prince Harry and Meghan Markle in the background during her televised Christmas address, further demonstrating that Markle, an American divorcee, has been welcomed into the Royal Family. They traditionally exchange gifts on Christmas Eve.
The British media has said Markle's stay at Sandringham with other royals is a sign of how quickly the royal family has accepted her.