Following the service, the extended family is expected to stay for lunch afterward with the Queen, who is also celebrating her 93rd birthday, in the castle.
Meghan, 37, who is due to give birth to her first child shortly, was not at the service, nor was the Queen’s husband Prince Philip, 97, who has retired from public duties.
On Sunday morning, the Queen was driven to the chapel where 16 members of the royal family, as well as an 800-strong congregation, awaited her arrival.
While waiting for the monarch, Harry was seen talking to Zara and exchanging pleasantries with Kate, but did not say anything to his elder brother.
Royal family members in attendance also included Princess Anne, her husband Vice Admiral Sir Timothy Laurence, Prince Andrew and his elder daughter Princess Beatrice, the Earl of Wessex with their children, Lady Louise Windsor and James, Viscount Severn. Zara and Mike were joined by Peter Phillips and his wife Autumn.
As the Queen, who wore a mink green coat with a matching hat adorned with a pink ribbon, walked into the chapel, the royal ladies all curtsied deeply.
Additionally, all the royal men, with the exception of William, bowed their heads.
William and Kate, who re-wore the light blue Alexander McQueen outfit she last wore during a 2014 trip to Sydney on Easter Sunday, were on time to this year’s ceremony, after arriving late to the service last year. (Kate, who was pregnant at the time with the couple’s third children, gave birth to son Prince Louis just days later).
After the Queen made her way inside the chapel, the rest of the royal family followed suit. The hour-long service was led by the Right Reverend David Conner, Dean of Windsor.
In a sweet nod to the other big celebration taking place on Sunday, after the family all took their seats, the organist played “Happy Birthday To You” in honor of the monarch’s big day.
The Queen, who was born on April 21, 1926, has two birthdays. She also has an official one on the second Saturday in June each year, which is commemorated with the Trooping the Colour parade.
Although there was no mention of the royal birthday in the sermon, the Dean did touch on the devastating fire at Notre-Dame Cathedral in Paris last week. He also read some Easter poetry by Christian socialist Charles Kingsley, author of The Water Babies, whose birth 200 years ago will be celebrated in June.