Three years later, they relegated to A2 Ethniki, but they were promoted back to the top-tier level the following season.

As the years passed, the team became stronger and they won two consecutive Greek Handball Championships in 2009 and 2010.

In 2009–10 season, PAOK became the second Greek team after Filippos Veria, who reached the EHF Champions League group stage.

In 2011, even though PAOK needed only a draw in the last home game in Thessaloniki to secure their third consecutive title, they lost the championship to AEK.

In 2024, PAOK won 21–20 against Drama and earned their fourth Greek Cup title.