The monarch accepted flowers, cards and presents from the hundreds of people wanting to wish her well on the milestone.
The Queen was dressed in what was described by Buckingham Palace as a "spring grass green" wool and silk weave coat and dress with hat to match adorned with flowers by her dressmaker Angela Kelly for her birthday appearance.
Her arrival was marked by a rendition of Happy Birthday by the Band of the Coldstream Guards.
She was accompanied by her husband of more than 68 years, the Duke of Edinburgh, who himself turns 95 in June as she opened a walkway created in her honour.
The couple then went on to meet other nonagenarians, including Chelsea Pensioners, inside the town's Corn Market.
The Queen was also presented with a cake by Great British Bake Off winner Nadiya Hussain.
They were then driven around the streets of Windsor in an open-topped Range Rover so they could wave at the cheering crowds.
Earlier the King's Troop Royal Horse Artillery rode their horses and gun carriages past Buckingham Palace to Hyde Park to stage a 41 Gun Royal Salute at midday.
Prince Charles and David Cameron were among the first people to publicly wish the Queen a happy birthday.
The Prince of Wales recorded a passage from William Shakespeare's Henry VIII to mark his mother's milestone.
He chose an edited extract from a speech by Archbishop Thomas Cranmer to King Henry VIII after the birth of the future Queen Elizabeth I.
The heir to the throne said: "She shall be, to the happiness of England, An aged princess; many days shall see her, And yet no day without a deed to crown it."
The Prime Minister reflected on the Queen's 64-year reign saying: "Her Majesty has devoted her entire life to the service of others.
"Representing our country and carrying out all her duties with extraordinary grace and humility.
"Rarely has anyone in public life served so long, served so brilliantly, worked so hard and brought so many people together.
"And in this modern Elizabethan era in which so much around her has changed, Her Majesty has been steadfast, a rock of strength for our nation, for our Commonwealth and on so many occasions, for the whole world."
Mr Cameron has also spoken in the House of Commons where Labour leader Jeremy Corbyn also paid tribute.
The PM said: "Her Majesty's carried herself with the most extraordinary grace and humility.
"When people meet the Queen they talk about it for the rest of their lives.
"She understands that and really shows an interest in everyone she meets. They can really see that she cares."
During Mr Corbyn's speech he joked: "In her reign, Mr Speaker, she's seen off 12 prime ministers.
"I admire her energy, wish her well in her continuing and outstanding commitment to public life. I wish her a very happy 90th birthday."
The Houses of Parliament will be lit up red, white and blue in honour of the Queen's birthday.
In the evening, the night sky over her Berkshire home will be lit up by a beacon, started by the Queen, the first in a chain of more than 1,000 that will spread across the country and the globe.
The monarch's birthday has been marked by the release of a historic photograph of the Queen surrounded by her five great-grandchildren - including Prince George and Princess Charlotte - and her two youngest grandchildren.