In 2001, he joined Empoli, being a protagonist of the Tuscans' successful 2001–02 Serie B campaign which saw the team being crowned league winners under head coach Silvio Baldini.
After being released by Palermo in June 2004, Atzori chose to retire from football and instead focus on a management career, becoming Silvio Baldini's assistant at Parma.
[1] In June 2008, Atzori left Catania to accept a head coaching offer from Lega Pro Prima Divisione side Ravenna, a team where he had already spent four seasons as a player.
[5] After a disappointing start of season, with Sampdoria in seventh place despite being tipped as one of the leading direct promotion candidates during pre-season, Atzori was ultimately sacked on 13 November 2011.
[8] He successively served as head coach of Serie B club Pro Vercelli from December 2017 to January 2018, in a short but unsuccessful stint in charge of the Bianche Casacche.