After starting the first nine games, Koppen's 2005 season was derailed by a shoulder injury suffered in a November 13 game against the Miami Dolphins. He was placed on injured reserve following the game. In the 2006 season, Koppen returned to his role as the Patriots' starting center. On October 12, 2006, the Patriots announced that they had signed Koppen to a five-year, $20 million contract extension. He finished the year with all 16 starts, allowing two sacks and only committing two penalties all year.