"This decision was extremely difficult to make," Edu stated on Arsenal's official website.
"I've loved working with so many great colleagues across our men's, women's and academy teams, especially Mikel, who has become a great friend.
"Now it is time to pursue a different challenge. Arsenal will always remain in my heart. I wish the club and its supporters only good things and all the very best."
Edu arrived back in London five years ago after spells as sporting director at Corinthians and a similar role with the Brazilian national team.
He oversaw a clear out of ageing stars such as Mesut Ozil and Pierre-Emerick Aubameyang to make way for a younger squad that has thrived under Arteta's leadership, albeit with little silverware to show for it.
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Arsenal have not won a trophy since lifting the FA Cup in 2020, but finished second to Manchester City in each of the past two Premier League seasons.
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(This story has not been edited by staff and is auto-generated from a syndicated feed.)