Bonera signed for Brescia in 1995 and played at the youth teams of Brescia until the end of 1998–99 season, where he made his first team debut for Brescia in 1999–2000. He played a total of 72 games in his three seasons with Brescia.[2]
Bonera signed for Parma in July 2002. He played 32 Serie A games and scored a goal during his first season at Parma in 2002–03. In his following three seasons with Parma, he played 98 games of which 82 were in the Serie A. On 28 July 2006, Bonera moved to AC Milan[2] in a €3.3 million transfer deal.[3]
After a ten-month injury lay-off, Bonera made a successful 45-minute comeback against Novara in the Coppa Italia on 13 January 2010. Because of Milan's great central defensive partnership of Alessandro Nesta and Thiago Silva, Bonera was deployed at his former position, right back. He slotted in well, playing much better in that position than when he first joined Milan. Because of this, Bonera became Milan's starting right back, but when Gianluca Zambrotta, Luca Antonini and Massimo Oddo all returned from injury, he lost his starting place in the position. When Nesta once again found himself on the treatment table, however, coach Leonardo chose Bonera to fill in for him in central defence.
On 23 May 2013, amid speculation of a move to Juventus, Bonera signed a new contract with Milan until 30 June 2015. During these two years, he mainly played as a backup player to first-choice centre-backs Philippe Mexès and Alex.
At the end of his deal with Milan in the summer of 2015, Bonera was released and was linked with a move to newly promoted Carpi,[5] though he instead joined La Liga club Villarreal.[6] On 9 July 2019, after spending four seasons at the club as a backup option, he announced his retirement.[7]
On 9 July 2019 Bonera was announced as part of Marco Giampaolo's new coaching staff at A.C. Milan, rejoining the club as an assistant coach.[8]
He was confirmed also following the appointment of Stefano Pioli as new head coach. In November 2020, after both Pioli and assistant Giacomo Murelli were diagnosed positive for COVID-19, Bonera acted as interim head coach for the club on a temporary basis.[9]
After five years as an assistant, on 27 June 2024 Bonera was unveiled as the inaugural head coach of Milan Futuro, AC Milan's reserve team.[10]
He was called up to 2006 FIFA World Cup squad as one of the four emergency reserve players,[13] but after Gianluca Zambrotta was confirmed to be fit, Bonera was excluded from the final 23-man squad and sent home.[14]
After the 2006 World Cup, he was re-called for the first time under new manager Roberto Donadoni, ahead of the UEFA Euro 2008 qualifier against Scotland, a match scheduled for 28 March 2007.[15] However, he had to withdraw due to injury.[16] In October and November 2007, he was called up again.[17][18] He played in a 2–0 friendly win against future 2010 FIFA World Cup hosts South Africa with an experimental Italy squad,[19] and also came on as a substitute for Fabio Cannavaro in a 3–1 home win in a Euro 2008 qualifier against the Faroe Islands.[20] He was not selected for Euro 2008.[21]
After Marcello Lippi became Italy coach for the second time, Bonera was re-called in Lippi's first few matches,[22][23] but was later left out of his squad due to injury.[24] After the injury, Bonera was called up to the last friendly before the formal announcement of Italy's 2010 World Cup squad, against Cameroon.[25][26] However, he failed to enter both the preliminary World Cup squad on 11 May and the training camp on 4–5 May.[27]
Usually deployed as a centre-back, in his prime, Bonera was known for his pace, physical strength, and versatility as a defender, and was also capable of playing as a full back on either side of the pitch.[28][29]
^"Comunicato Ufficiale N. 28" [Official Press Release No. 28] (PDF) (in Italian). Lega Serie A. 19 August 2011. p. 2. Archived from the original(PDF) on 29 October 2021. Retrieved 11 December 2020.
^ abCarminati, Nadia (28 July 2006). "Milan bag Bonera". Sky Sports. Retrieved 13 May 2010.