Crucial goals against eventual champions Panathinaikos and AEK Athens in 2003–04 endeared him to supporters. Stoltidis also relished his first taste of UEFA Champions League football, scoring twice in five appearances. A regular in Dusan Bajevic's side in 2004–05, he played 25 league matches and scored twice. He appeared in all 540 minutes of the Champions League campaign and scored the winner at home against eventual champions Liverpool F.C.. In the same season, he won the Alpha Ethniki as well as the Greek Cup with Olympiakos.