The royal couple were among those who travelled to Balmoral Castle, where the 96-year-old is reported to have taken her last breath.
Duke, Duchess of Sussex honour Queen Elizabeth II
They updated their website to only show their tribute to the queen with a black background.
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“In loving memory of Her Majesty Queen Elizabeth II, 1926-2023,” said the write up on the website.
The two also did the same when the late Prince Phillip died, and they showered praises on him via their foundation’s site.
Harry and Markle have had a strained relationship with the royal family since the two walked down the aisle and took up royal duties.
In early 2021, the couple had a tell-it-all sitdown session with media mogul Oprah Winfrey where they narrated their challenges with the other royal family members.
Markle claimed top royal officials were worried about the colour of her then the unborn child and asked if the baby would be black.
The mother of two also talked about their decision to step down from their roles as royalties and how life changed for them since they embarked on a different path.