"It's been a special journey. I've loved working with excellent colleagues in the men's, women's and youth teams, especially Mikel (Arteta), who has become a great friend.
"Now it's time to look for a different challenge. Arsenal will always remain in my heart," said Edu, speaking on the club's media channels.
Edu's departure from the Gunners is due to the new project he has ahead of him, with the Brazilian reportedly set to work under Nottingham Forest owner Evangelos Marinakis as a director for the Greek businessman's network of clubs, which currently consists of Olympiacos and Rio Ave as well as Forest.
"We respect Edu's decision and thank him for his immense contribution and dedication to drive the club forward," Arsenal co-chair Josh Kroenke said.
"Change and evolution is a part of our club. We remain focused on our strategy and winning major trophies. Our succession plan will reflect this continued ambition."
The Brazilian manager, who was part of Arsene Wenger's 'Invincibles' squad, returned to Arsenal in 2019 to take on the role of technical director.
Since 2022, he had been in charge of their men's and women's teams, as well as youth football.
Together with coach Mikel Arteta, Edu was responsible for the recent reorganisation and revival of Arsenal, who have begun challenging for the Premier League title again in the last two years.