The pre-season started with several major changes, the biggest being the sacking of coach Christian Gross, who was replaced by the German Thorsten Fink. Fink was appointed as Basel's new manager on 9 June 2009. The new manager let several players go by not extending their contracts. These were Ronny Hodel, Jürgen Gjasula, Ivan Ergić and Eduardo. Star striker Eren Derdiyok was sold to Bayer 04 Leverkusen and Eduardo Rubio returned to Cruz Azul because his loan was not made permanent. A number of players were brought into the first team from the under-21 squad to replace them, including Xherdan Shaqiri, Marco Aratore and Oliver Klaus. A number of new players were signed, the highest profile being Alexander Frei from Borussia Dortmund. Others new signings included TurkishÇağdaş Atan from Energie Cottbus, Ghanaian Samuel Inkoom from Asante Kotoko, Massimo Colomba from rivals Grasshopper, Brazilian Antônio da Silvaon loan from Karlsruher SC and Cabral who returned after being on loan to Sevilla. Basel entered the Europa League in the second qualifying round and were drawn against Andorrans Santa Colma. The first leg was at home in the St. Jakob-Park, in front of over 25'000 spectators, and ended 3–0 in Basel's favour, with Serkan Şahin, Marco Streller and Federico Almerares getting on the score sheet. The second leg at Estadi Comunal d'Aixovall ended with a 4–1 victory for Basel, thus victors with a 7–1 on aggregate. Streller, Marcos Gelabert and Almerares scored the goals the second time around. FCB were then drawn against KR Reykjavík of Iceland in the third qualifying round. The first leg took place at KR-völlur on 30 July, and ended in a 2–2 draw. Early goals from Gudmundur Benediktsson and Grétar Sigurdsson gave the home side a 2–0 lead, before Scott Chipperfield and Almerares drew Basel level. The second leg in Switzerland ended with a 3–1 win for Basel, meaning they won 5–3 on aggregate and progressed to a two-legged play-off against FK Baku of Azerbaijan. Alexander Frei and Xherdan Shaqiri scored for FCB and Björgólfur Takefusa scored for the Icelanders. At the Tofik Bakhramov Stadium in Baku, Fernando Nestor Pérez put the locals 1–0 ahead just after half time. Basel turned it around, however, and won 3–1 scoring three goals in six minutes, these coming from Streller and Benjamin Huggel. The second leg at home ended with Basel winning 5–1 on the night and 8–2 on aggregate, meaning that they qualified for the Europa League group stage. Almerares, Gelabert, Frei, Shaqiri and Orhan Mustafi all contributed with Basel's goals while Felipe Almeida Félix scored for the away side. In the group stage FCB were then drawn into Group E alongside A.S. Roma, Fulham and CSKA Sofia. Basel started in the group with an impressive 2–0 win over Roma at home – Carlitos and Federico Almerares scoring the goals on 17 September 2009 – before narrowly losing their second match 1–0 in a tight encounter with Fulham at Craven Cottage on 1 October. Their third match took place on 22 October and was against CSKA Sofia at the Vasil Levski National Stadium. Frei scored two goals there to send Basel home with a 2–0 win. They also won the return leg, on 5 November 3–1. Frei again scoring two goals, with Gelabert scoring the other. Todor Yanchev scored for the visitors. After this, they lost 2–1 to Roma away, leaving their fate hinging on the final match against Fulham at home. In a close game, the English club narrowly won 3–2, sending Basel out with third place in the Group Table. In domestic affairs, Basel swept the board, despite a poor start to the season. During the seasons winter break they were thirteen points behind the leaders, but FCB came back with 14 victories in the las 16 games, to win the title on the last day of the season. This match was in Bern at the Stade de Suisse against favourites BSC Young Boys. Young prospect Valentin Stocker and club legend Scott Chipperfield gave Basel the goals in the 2–0 win on 16 May. In the 2009–10 Swiss Cup final, on 9 May, FC Basel achieved an outstanding 6–0 victory over FC Lausanne-Sport, with Stocker scoring twice, and Shaqiri, Zoua, Chipperfield and Huggel also getting onto the scoreboard. The win secured FC Basel's tenth Cup win to date.
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First team
As of 7 October 2009, accounting for official transfers:
Marco Streller
Scott Chipperfield
Federico Almerares
Antônio da Silva
Jacques Zoua
Carlitos
Çağdaş Atan
Behrang Safari
Samuel Inkoom