On 31 August 2010, he was signed by Italian Serie A team Bologna for €2.1 million (including 5% solidarity contribution to youth clubs). No fee was scheduled to pay on that day, but 2 equal installments was scheduled on 31 December 2010 and 30 June 2011. At Bologna, he has teamed up with fellow Uruguayan internationals, Henry Damián Giménez, Gastón Ramírez and Miguel Britos, before this left the squad to join S.S.C. Napoli. In Pérez first season in the Serie A, Bologna managed 16th place and finished six points clear of relegation, confirming a fourth successive season in the Italian top flight. He also managed three assists during the campaign, tied for most on the team along with Riccardo Meggiorini.