On 14 July 2004, he left AEK Athens for Bologna, signing a two-year contract worth €1.5 million per year. The 32-year-old midfielder – who was voted player of the tournament in Portugal – was released by debt-ridden AEK Athens and joined Bologna on a Bosman free transfer. "Zagorakis is our Greek Baggio", Bologna owner Giuseppe Gazzoni Frascara told the newspaper. In 2004–05, Zagorakis was a regular feature in the squad, but the team found itself relegated to Serie B after a play-out series against Parma. In the following summer, he was released from the team as they couldn't afford his payroll under the new conditions.