In 2007, the team advanced to the first tier, where they still are today. The first season back the team finished 14th place with 27 points. The following year was better where the club finished 8th with 34 points. In 2009, the club was punished with a deduction of 10 points following a corruption scandal, committed by the previous president of the club. The first success of the club was the 2009–10 season where Jagiellonia won the Polish Cup, beating Pogon Szczecin thanks to a goal from Andrius Skerla. The 2014–15 season was the second most successful season Jagiellonia saw finishing 3rd place. In the 2016–17 season Jagiellonia were runners up for the first time in the club's history. Jagiellonia won the Polish Cup and finished 3rd and 2nd when coached by Michał Probierz.