After spending seven years at Udinese, Jørgensen moved to league rivals Fiorentina in August 2004, when the club bought half of Jørgensen's transfer fee rights. He proved to be a key asset to Fiorentina's offensive play and became beloved by the fans. As an attacking midfielder, he played close to the two strikers and during the 2007–08 season he also served as a right back for the majority of the season. He had important contributions for Fiorentina during that season, scoring two goals in the UEFA Cup fixture against IF Elfsborg, and being a key part of the 3–2 win over Juventus on 2 March 2008.