During Basel's 2008–09 season, Huggel showed his goal scoring qualities. Basel played their opening game of the season in Bern on 18 July 2008 against BSC Young Boys, which they won 2–1. Basel's goals were scored by Marko Perović and Benjamin Huggel. Basel entered the Champions League in the Second Qualifying Round and were drawn against IFK Göteborg of the Allsvenskan. The first leg was on 30 July 2008 at Ullevi and finished 1–1. Huggel scored the Basel goal. The second leg was played on 6 August at St. Jakob-Park. Basel came from behind twice to win 4–2, Huggel scored the equaliser to 1–1, and Basel qualified for the UEFA Champions League Group Stages against FC Barcelona, FC Shakhtar Donetsk and Sporting Clube de Portugal. In the League. despite remaining in first or second position for most of the season, Basel finished only in third position behind FC Zürich and Young Boys. Huggel scored ten league goals that season, only second behind Scott Chipperfield, who scored 12 times.