The 2006–07 season saw Nolan take over from the departed Jay-Jay Okocha as club captain. His three league goals helped Bolton to again qualify for the UEFA Cup. Nolan's long throw-in set up a goal, which helped Bolton achieve a 2–2 draw away against German champions Bayern Munich, who dominated the match. Despite reaching the first knockout round, Bolton's league form suffered as they were pulled into a relegation fight, eventually finishing the season one point above the relegation zone in 16th. Nolan scored in the 2–0 win over Sunderland in May that virtually secured the club's Premier League status.