However, he struggled with a niggling injury in the second half of the 2008–09 season, joining Alessandro Nesta and Kakha Kaladze on the treatment table.

[4] 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.

When Nesta once again found himself on the treatment table, however, coach Leonardo chose Bonera to fill in for him in central defence.

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.

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.

[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.

[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.

[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.