Markle will be baptised and confirmed for the wedding and intends to become a British citizen, Harry's spokesman Jason Knauf told reporters.
Knauf said Windsor, Queen Elizabeth II's weekend residence, was a "very special place" for Harry and that he and Markle had spent time there together.
He said the couple would be putting their personal stamp on their wedding day, adding: "They will be making sure it reflects who they are as a couple."
Kensington Palace, Harry's official residence, said in a statement: "Her Majesty The Queen has granted permission for the wedding to take place in the chapel. The Royal Family will pay for the wedding."
The two will be visiting the city of Nottingham in central England on Friday for their first trip together since announcing their engagement on Monday.