Following the unexpected loss of the Championship of the previous season, the club, as well as its supporters were trying to recover from the shock. Furthermore, on 10 June,
Dimitris Melissanidis announced his departure from the ownership of the club after 11 years, which handed it over to shipowner,
Marios Iliopoulos. The new management left full control of the transfers to
Matías Almeyda and proceeded with the signings of prominent footballers, such as
Thomas Strakosha,
Roberto Pereyra,
Erik Lamela,
Aboubakary Koïta and most notably
Anthony Martial, while from the domestic market they acquired
Alberto Brignoli,
Moses Odubajo and
Sotiris Tsiloulis. Among the departures were
Georgios Athanasiadis,
Djibril Sidibé,
Tom van Weert,
Ezequiel Ponce and most notably their captain for the past two seasons,
Sergio Araujo. However, Iliopoulos after two months at the wheel, reorganized the football department of the club by hiring
Javier Ribalta as its director. AEK began their European journey in the second qualifying round of the
UEFA Conference League by facing
Inter Club d'Escaldes. Despite a problematic 4–3 victory at home, they secured the qualification in the rematch with a 0–3 win. In the following round AEK came across
Noah. After a shameful performance at
Armavir City Stadium, which resulted in a 3–1 defeat, they were eventually eliminated by the Armenian club, following their 1–0 win at
Agia Sophia Stadium. The early elimination of the club sparked doubts about Almeyda. The differences between the philosophies of Almeyda and Ribalta became evident during the winter transfer window, when
Konstantinos Galanopoulos,
Nordin Amrabat,
Steven Zuber and
Levi García left the club, but no gaps within the roster were filled, as the club did not make any signings whatsoever. In the Championship AEK displayed great performances at times, but two consecutive away defeats removed them from the top of the table. AEK were suffering from constant injuries of key players, as well as by the way the team was treated by Greek referees during their matches. The combination of these negatively affected the high-pressure game that Almeyda was applying throughout his previous seasons within the team. Furthermore, on 26 November, AEK faced
Olympiacos at
Karaiskakis Stadium and suffered an embarrassing 4–1 defeat that showed that the playing style of Almeyda was no longer unmatched. The defeat was met by further doubts for the manager, but the majority of the supporters continued to support the club and Almeyda, which was prooved at the 4–0 home win over
Aris in the following matchday. However, on 19 January 2025, after a 1–0 defeat to
Panathinaikos, Almeyda spoke with uncertainty about his future at the club. This resulted in an arrangement of a meeting between Almeyda and Iliopoulos, where it was decided that the Argentine manager would continue at the club. Afterwards, AEK displaying consistent performances, achieved a five-match winning streak and emerged as the only title contenders, behind Olympiacos. One of these was a 1–2 win at
Toumba Stadium, where Lamela scored both goals, while the first was voted as goal of the season in the Super League. Their hopes of claiming any title in the season collapsed, when AEK lost at home to Olympiacos in the penultimate matchday. As in the previous season, AEK entered the Cup at the round of 16, facing Aris. This time however, they managed to overcome their opponent and with a 1–0 win in
Athens and a 1–1 draw in
Thessaloniki, they qualified to the next round. In the quarter-finals, they came against PAOK. After the end of the match at Nea Filadelfeia Stadium which ended 1–0 for the yellow-blacks, the officials of PAOK reported an attack on their bus by ultras in the parking of the stadium. However, as the security cameras showed, while the squad of PAOK were departing, three supporters of AEK were showing to the squad a yellow-black shirt of the
2018 Championship conquest. The officials of PAOK, starring their manager
Răzvan Lucescu, got off the bus in a furious state and physically and verbally attacked the three supporters. The Romanian manager and four other members of the staff were punished with a 4-month ban from the stadiums, which was reduced on appeal to 45 days. In the rematch, PAOK managed to equalize the score of the first match, which sent the match to extra time, however, AEK eventually took the qualification at the 107th minute, with a goal by Odubajo. In the semi-finals, AEK faced Olympiacos. The first match at
Piraeus was a complete disaster, as AEK appeared completely unprepared, both competitively and mentally and made lots of mistakes, which Olympiacos took advantage of and scored six goals from as many shots on target. The rematch at
Nea Filadelfeia was merely procedural and AEK won by 2–0. The harsh elimination caused a rift among the supporters of AEK referring the presence of Almeyda at the team's bench. In the play-offs, Olympiacos had gained a 7-point lead over second-placed AEK and the big interest was the final standings and the tickets for European competitions. Even though AEK started with a significant 4-point lead over Panathinaikos and a 7-point lead over PAOK respectively, the situation created by the negative results against Olympiacos, resulted in the team being in a mental and competitve collapse. Thus, AEK finished at the fourth place, losing all six matches of the round, achieving a negative record. After the end of the season, Almeyda met for the last time with Iliopoulos and the following day his contract was terminated. Despite the negative situation, the Argentine manager he had a warm farewell from the ultras at the airport. ==Management team==