Bonera's UEFA Champions League came against Belgian side Anderlecht on 17 October 2006, in which he received a red card after receiving a second yellow in the 47th minute for what, in the referee's view, was petulantly kicking the ball away as Anderlecht waited to take a free kick. After struggling at right back, Bonera was moved to centre back after several defenders were injured, and after the acquisition of Massimo Oddo from Lazio in January, a natural right back. Bonera slotted in well at centre back, becoming one of Milan's better players. 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. In September 2009, he signed a contract extension which will last until 2013.
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. However, he had to withdraw due to injury. In October and November 2007, he was called up again. He played in a 2–0 friendly win against future 2010 FIFA World Cup hosts South Africa with an experimental Italy squad, 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. He was not selected for Euro 2008.