The former defender announced his retirement at Villarreal this week and has returned to Milan, where he played from 2006 to 2015.
The 38-year-old will be working as one of coach Marco Giampaolo's assistants, joined by Francesco Conti, Salvatore Foti and Fabio Micarelli.
Stefano Rapetti is the fitness coach, Luigi Turci the goalkeeping coach and Emiliano Betti his assistant.
Bonera made 201 competitive appearances for the Rossonero.
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