Jason Knauf will step down as chief executive of the Royal Foundation at the end of the year, a statement said on Wednesday.
Mr Knauf was the royal adviser who first reported Meghan Markle for alleged harassment in 2018, according to the Times.
He moved to work with the Cambridges in 2019, after the Sussexes left the royal family.
Mr Knauf is said to have lodged a complaint against Ms Markle’s behavior towards other assistants, which would have forced Prince Harry to intervene.
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Reports say the Duchess “kicked two personal assistants out of the house”, while “undermining the confidence of a third staff member”.
Ms Markle denies the allegations and her team issued a harsh statement following the accusations, describing them as “a calculated smear campaign based on misleading and harmful disinformation.”
A spokesperson for the couple also said Harry would not interfere in the affairs of the staff
Mr. Knauf joined the Kensington Palace communications team in 2015 before taking up his post with the foundation in 2019.
In a joint statement on his departure, the Duke and Duchess of Cambridge said: “Jason has been an integral part of our team since 2015.
“We are extremely grateful for his hard work and commitment, both to the Royal Foundation and before as Secretary of Communications.
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“Since taking office as CEO, Jason has spurred positive change, making our vision for our charitable work and the causes that matter most to us a reality.
“We are sad to see him go, but we wish him good luck in his future career.
“We look forward to starting the recruitment search shortly and welcoming a new Managing Director later this year. “
Mr Knauf added: “Working with the Duke and Duchess of Cambridge has been the privilege of my career.
“I will always be grateful for the opportunity I had to support their leadership in the UK and internationally.
“The coming months will be the busiest times in the Foundation’s history with top prizes for the Earthshot Prize and more progress in our work on early childhood.
“We have a lot to do with our great team and all of our partners. “
A statement added that Mr Knauf “will remain in post until the end of 2021 before a planned international relocation which necessitated his decision to resign”.