She was presented with flowers and a crowd sang “Happy Birthday” as she left St George’s Chapel.
In an Easter message, Prime Minister Theresa May said the UK “must stand up for the right of everyone” to practise their faith in peace.
And Labour leader Jeremy Corbyn compared the experience of Jesus to the challenges facing some refugees today.
The Queen was joined for the Easter Sunday service by family members including the Duke and Duchess of Cambridge and the Duke of Sussex.
The Duke of Edinburgh, who has retired from public duties, and the Duchess of Sussex, who is heavily pregnant, did not attend.
But Prince Harry and Meghan posted a joint birthday greeting to the Queen on Instagram, saying: “Happy Birthday Your Majesty, Ma’am, Granny.”
As the Queen left the chapel, she was presented with two posies – one yellow and one white – by two boys.
Gun salutes will also be fired in London to mark her birthday – although she will have to wait a day, as they are never done on a Sunday.
The Queen celebrates two birthdays each year – 21 April is her actual birthday and she also has an official one on the second Saturday in June, which is commemorated with the Trooping the Colour parade.
The Archbishop of Canterbury, Justin Welby, used his Easter message to say the resurrection of Jesus showed injustice and oppression don’t have the last word.
The risen Jesus is the one who makes our broken lives whole, he said.
In her Easter message, the prime minister said she will spend her time giving thanks in church, but for many Christians such simple acts of faith can bring huge danger.
1,611 total views, 3 views today