As of the summer of 1997, AEK has been through continuous changes at all levels: from ownership and presidents (the first president under ENIC was the renowned orthopedist Pandelis Nikolaou, also a former glory of the team, but he was succeeded by Kostas Generakis in late 1998, whereas Stefanos Mamatzis took over in 1999) to the people running the company and the team. In the summer of 1998, the Serbian Dragoslav Stepanovic became coach, only to be succeeded by the Ukrainian Oleg Blokhin a few months afterwards, but in the summer of 1999, the Serbian Ljubiša Tumbaković was sitting on the bench. At that time, the Dutch company NETMED took over the FC's management.
The second half of 1999 was traumatic for AEK, although it started off enthusiastically and with good transfers, such as that of the Serbian midfielder Dragan Ćirić who was on loan from Barcelona. However, what came next was tragic: AEK was not only eliminated by AIK Stockholm in the Champions League qualifying rounds, but the September earthquake greatly damaged the Nea FIladelfia Stadium and forced the team to move from one home ground to another for a long time. In one of the few matches played on its home ground, it was subject to the criminal decisions of Dimitropoulos, a referee from Patras, in a derby against Olympiacos, and it paid the price for subsequent incidents with harsh penalties both on the team and players (Kasapis).
In early 2000, the memorable Giannis Pathiakakis replaced Tumbaković and the team showed spectacular improvement, since the season ended with AEK winning the Greek Cup by defeating Ionikos 3-0 in the final at OAKA. That was also the score in the quarterfinals when AEK defeated Olympiacos.
In the summer of 2000, a top-level NETMED executive, the Dutch Cornelius Sierhuis was president, and Pathiakakis was coach. The team made an ambitious start with important transfers (Tsiartas returned, Navas was acquired, Ruiz came from Boca Juniors and Ferrugem from Palmeiras), but the campaign was not good. The qualification against Leverkusen was just a flash in the pan, since shortly afterwards it was necessary to change the coach, and Toni Savevski became coach overnight having Eugène Gerards by his side. AEK got better, but finished in the 3rd position.
In the summer of 2001, AEK FC was transferred in the hands of Makis Psomiadis. ENIC continued to hold the shares, but the controversial businessman ran everything. When he was shown to the door in February 2003, after the incident outside the house of the then AEK footballer Demis Nikolaidis, he left having embezzled funds, which brought AEK to the edge of the cliff.
Among the few good times are the Cup title in 2002 after a 2-1 victory over Olympiacos at OAKA, the championship campaign, although the title was lost to the said opponent after a tie, with Fernando Santos as coach and the six ties in the 2002-03 Champions League group, with Dusan Bajevic as coach, when AEK finished 3rd in its group, however, it made history after the 3-3 at Nea Filadelfia against the "Galactic" Real Madrid of Zidane, Raul, Figo, etc., and the 2-2 that overturned the 2-0 at Bernabeu. The other ties were against Roma and the Belgian champion Genk.
However, the year-long poor management and, particularly, the tenure of Psomiadis had given rise to serious problems. Summer of 2003 was a season of agony over whether or not the FC would be allowed to compete in the championship. Moreover, the then caretaker president, Giannis Granitsas, decided to demolish the stadium, leaving AEK homeless, unfortunately, to date.
The Granitsas plan for a multi-purpose stadium having huge shopping areas was hindered by protests of Nea Filadelfia residents and the lack of resources, whereas the then president of Olympiacos, Sokratis Kokalis managed to have the new Karaiskakis stadium included in the 2004 Olympic Games projects in the place of AEK's stadium, as was originally planned. AEK was homeless after 73 years and without having ensured its future home ground, as proven along the way.
The 2003-04 season was tragic. AEK competed in the Champions League, but only earned two points in a group with La Coruña, Eindhoven, and Monaco, using the Leoforos Stadium as its home ground. In the championship, it wandered between five different home grounds (Nea Smirni, Ano Liosia, Leoforos, Tavros, Kallithea) and faced with huge financial problems, it failed to meet all objectives early on. However, Demis Nikolaidis was already preparing a rescue plan from Madrid, where he was playing for Atlético.