The start of the new millenium finds PAOK winning earing yet another place in Euroleague, but first has the team finding a new arena. PAOK Sports Arena opens its gates, but the team's relocation in it will be in the middle of unfortunate events that will put a stop to the previous years' success. With a new owner, the president of the football team at the time, Giorgios Batatoudis, a roster worth hundreds of millions of drachma (Sigalas, Liadelis, Koronios, Coldebella), Giannoulis as the captain, Kostas Flevarakis back as coach (with whom the team had won the Cup in '99) and many dreams, PAOK starts the 2000-01 season with goals of winning European titles, but after a while, the dream turns into a nightmare.

The same luck would find all ensuing efforts. The special debt settlement with the government left a sour taste for all. The team goes through a lot of tough times, with huge financial problems and from the 2001-02 has a court administration with Vassilis Oikonomidis as president, Lefteris Subotic as the team's coach at the start of the season and Vaggelis Alexandris coaching at the end of it. The debt settlement gives PAOK the ability to start over again, and that's exactly what happens. With a core of young players (Vassileiadis, Vassilopoulos, Mavrokefalidis), Bane Prelevic as Head Coach and from January 17 2004 Takis Paneloudis as the owner of the newly formed B.C., PAOK starts all over. The effort doesn't end like one would expect and mostly the fans that supported the team as always for the new beginning.