Thorsten Fink was appointed as Basel's new manager on 9 June 2009. Basel entered the Europa League in the second qualifying round playing against Andorrans Santa Colma, against KR Reykjavík of Iceland in the third round, against FK Baku of Azerbaijan in the play-offs and they qualified for the Europa League group stage. FCB were then drawn into Group E alongside A.S. Roma (Serie A), Fulham (Premier League) and CSKA Sofia (Bulgarian A Professional Football Group). But they only finishing in third place. Huggel played all twelve Europa League matches. In domestic affairs Basel swept the board. Despite a poor start to the season they came back to win the title on the last day of the season in the match against favourites BSC Young Boys at the Stade de Suisse. Huggel played 32 League matches, scoring eleven goals. At the end of Basel's 2009–10 season Huggel also won the Swiss Cup and yet again he scored a goal in the cup final as they beat Lausanne-Sport 6–0. At the end of the season, the goal that Huggel scored in the 2–2 away draw on 28 October 2009 against Zürich was voted "Best European Goal of the Season 2009–2010" on guardian.co.uk, where it was chosen by a massive lot of over 84%.