The Brazilian was promoted to the role in November 2022, having previously been technical director.
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Edu, an ex-player who won the Premier League at the club, was an ally of manager Mikel Arteta.
Per Sky Sports News, he is being lined up for a role within owner Evangelos Marinakis' clubs, which include Nottingham Forest.
According to the Independent, Edu has been talking with Marinakis and is ready to take a job with him.
Arsenal will be disappointed to have lost him and will now have to begin the search for a replacement.
