As he did not immediately accept the offer the management became suspicious and decided to relegate him to the bench for the rest of the 2003–04 season.

The Greek sports media and Panathinaikos fans at first took his side in the conflict and criticised president Vardinogiannis.

After that, the fans' disappointment in him was displayed during the celebrations following the team's 2003–04 season double when Nikopolidis, while raising the trophy, was booed by the majority of the crowd.

Soon after being instrumental in UEFA Euro 2004 helping Greece to lift the trophy, Nikopolidis joined Olympiacos, making an immediate impact for his once rival team.

[4] On 20 March 2011, Olympiacos won the championship in a 6–0 win against rivals AEK Athens F.C., in Karaiskakis Stadium.

As a final curtain call, he was replaced by Balázs Megyeri in the last minutes, so he could wave goodbye to the Olympiacos fans.

On 15 June 2008, Nikopolidis announced his retirement from international football after Euro 2008, claiming that he had made this decision before the tournament started, and also stating that it is about time for a major change in the Greece national team.

Despite not being particularly tall or agile, his excellent positional sense made him an effective shot-stopper and his ability to read and understand the game helped him rush quickly off his line in order to face one on one situations or act as a sweeper-keeper.