On the opening day of the 2008–09 Serie A season, İnler scored the third goal of a 3–1 win over Palermo and provided an assist for one of Antonio Di Natale's two goals. On 18 September, İnler then scored in the first leg of a UEFA Cup qualifying round game away against Borussia Dortmund, a game Udinese won 0–2. Despite then losing the home leg 0–2 courtesy of two goals from Tamas Hajnal, Udinese progressed after winning 4–3 in penalties, with İnler converting his kick. İnler featured in all four of Udinese's group stage games as they finished first in their group with nine points. In the Round of 16, İnler started both legs against reigning champions Zenit Saint Petersburg, as Udinese won 2–1 on aggregate against the Russians. In the quarterfinal round against Werder Bremen, Udinese lost the first leg 3–1 away from home, but in the second leg, İnler struck early on for the hosts, netting a dipping shot from over 25 yards out. Diego equalized for the Germans before Fabio Quagliarella netted twice before the break to bring the aggregate score to 4–4. Two second-half goals for Bremen, however, meant that the hosts were knocked out at the quarterfinal stage.