The former Sunderland chief is taking charge of Saudi Pro League club Al Ahli.
Atalanta announced last night: "Atalanta BC and Lee Congerton communicate the decision to consensually end their professional relationship with effect from tomorrow, Friday 1 March 2024. For two years the Welsh manager held the role of Head of International Development of the Sports Area.
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"Lee Congerton thanks the Percassi and Pagliuca families for the important and rewarding professional opportunity that has enriched his wealth of experience.
"The Percassi family, the Pagliuca family and all of Atalanta BC in turn express gratitude to Lee Congerton for the professionalism and dedication made available to the Club, at the same time wishing him the best luck for the future."