The Duke of Edinburgh joined the Queen at the dedication service at the Guildhall.
They were met by members of the Royal Albert Institute Trust and the team from Artemis Glass in Staines, who created the two windows.
The windows were the gift of the Royal Albert Institute Trust to the people of Windsor.
During the visit, the royals viewed a display of the early designs ideas, before viewing the completed windows.
Susanne Dickinson, who runs Artemis Glass with her husband, Michael, said the windows took eight weeks to make, from design to creation.
"It is quite an honour to have designed something that will be around for hundreds of years," she added.
"We are looking forward to the event but we are very nervous. It's quite a thing to meet the Queen.
"We knew a royal would unveil them but we didn't know it would be the Queen."