The Mirror says Ellis departed last week after being assigned the project of overhauling the club's academy setup.
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After Per Mertesacker's resignation as academy director, part of Ellis' brief was to find a replacement for the German.
He also leaves with a planned revamp of the development pathway completed and on the table.
Meanwhile, it's been suggested that former Chelsea youth chief Jim Fraser could soon be confirmed as Mertesacker's successor.
Further, current football chief Andrea Berta will see his powers expanded at Arsenal, with the Italian holding a greater influence and say on academy matters.