Middleton took over the Red Roses in 2015 and broke the Test win record with the team winning 30 matches in a row between November 2019 and November 2022.
"This is definitely the right time for someone to take over at the helm with new ideas and a different voice for players to get inspired by," Middleton said.
He received an MBE for services to rugby in June 2021 and was the first women's coach to be named World Rugby Coach of the Year that year.
"Representing England in a coaching or playing capacity must be the pinnacle of any sporting career and I can’t put into words how proud and fortunate I’ve been to be able to do this for the last nine years," Middleton added.
"I’ve seen a lot of change over the nine years I’ve been involved and the development of the women’s game has been remarkable."
