The high-profile event yesterday fell on the second day of the national commemorations marking the monarch’s milestone 70-year reign.
The 96-year-old Queen was absent, watching on television from Windsor Castle instead, after she suffered “discomfort” following a busy first day of festivities including a double balcony appearance and a beacon lighting.
It was the first time Harry and Meghan had been on full public view alongside the Windsors since they quit the monarchy for a new life in the US two years ago.
Crowds cheered the pair as they arrived, with the couple smiling and waving, but both boos and cheers could be heard as they departed.
They processed through the nave of the church hand in hand, with a smiling Meghan, dressed in an elegant trench coat from the Dior Haute Couture spring-summer 2022 collection by Maria Grazia Chiuri, a Stephen Jones hat and wearing white gloves, while Harry bit his lip at times.
The duke, dressed in a morning suit, was wearing his Platinum Jubilee medal, along with his Golden and Diamond Jubilee and Afghanistan campaign decorations.
Indicative of their new more-minor position within the royal family, they were sat in the second row from the front behind the Wessex family and the Duke and Duchess of Gloucester, with Harry next to Princess Eugenie’s husband Jack Brooksbank and Meghan next to Princess Margaret’s daughter Lady Sarah Chatto.
Across the aisle was Harry’s father the Prince of Wales, representing the Queen, and Duchess of Cornwall, in ornate chairs, and Harry’s brother the Duke of Cambridge and Duchess of Cambridge, the Princess Royal and her husband, Vice Admiral Sir Tim Laurence.
At one point, Harry was spotted with his mouth open, appearing to be enjoying a joke with other royals – most likely Zara and Mike Tindall – seated across the aisle.
Beatrice, sitting a few seats down, was also grinning in the same direction.
Harry was also seen laughing with Mr Brooksbank, and joined the Tindalls and cousin Peter Phillips for a chat on the steps afterwards.
The Sussexes attended the Trooping celebrations at Horse Guards on Thursday, but stayed out of the spotlight inside the Duke of Wellington’s former office with more than 30 members of the family.
More than 2,000 people filled the historic church including Prime Minister Boris Johnson, who was booed by the crowd outside, Cabinet ministers, Labour leader Sir Keir Starmer, first ministers of the devolved governments and every living former prime minister.
There were smiles from the royals and ripples of laughter from the congregation as the Archbishop of York compared the monarch’s well-known love of horse racing to her long reign, suggesting it “reflects the distance of Aintree more than the sprints of Epsom”.
The Queen was, the Most Rev Stephen Cottrell said, “still in the saddle”, as he thanked her for “staying the course”, with Olympic equestrian Zara smiling at the remarks along with the Earl and Countess of Wessex.