The season started without much hope for AEK, as it seemed that they were not able of claiming the championship. Many new players came with the most important being
Papa Bouba Diop, along with the return of
Dellas and
Liberopoulos. There were also quite a few departures, with those of
Majstorović and
Manduca standing out.
Dušan Bajević remained at the wheel of the club. The
Europa League group stage was vital for AEK, as they had not had a good start to the season. In a "convenient" draw for AEK, they came against the Scottish
Dundee United. At
Tannadice Park AEK, despite their mediocre performance, came away with the win, with a quick goal early in the match. Before the rematch, strange things happened with AEK even being at risk of being zeroed by
UEFA. Initially, the possibility of hosting the game at the
Olympic Stadium was ruled out, due to the upcoming concert of
U2 at the stadium and the error in the maintenance of the pitch, with the turf coming off with the slightest touch. In the search for a stadium for the match, they ended up at the
Nea Smyrni Stadium, but the incomprehensible and complex behavior of the ultras of
Panionios, who as soon as they learned that their team's ground was chosen, invaded their own stadium at night and caused damages by digging up the pitch, cutting the posts and destroying the irrigation system, making it unfit for a match. In the midst of a heavy atmosphere in AEK and the
HFF,
Olympiacos, through their vice-president
Giannis Moralis, proposed the
Karaiskakis Stadium, with the condition that AEK would not print tickets for the game, with the presence of only the Dundee fans in the stadium. Thus, AEK played away from their home, as if they were punished, losing significant income, without being responsible for any of this. Under these circumstances, AEK started strongly the match and scored in the first half. Bajević then decided to experiment with the players during the second half, with the team's performance dropping increasingly and the Scots going up front and taking advantage of AEK's indifference, they equalized and needed just a goal to qualify, which eventually never came. AEK were drawn in Group G along with
Zenit Saint Petersburg,
Anderlecht and
Hajduk Split, where they were eliminated on a draw with Anderlecht, after losing their last game to Zenit, finishing third. In the league, they started tragically with many defeats in the first 4 matches that led to the removal of Dušan Bajević and the hiring
Manolo Jiménez from
Sevilla. The new coach started with an emphatic 0–4 against
Aris and a victory over
Panathinaikos, but the defeat by Panionios the following matchday, ended any hopes of recovery. The rest of the first round was mediocre, as only the victory over Olympiacos stood out. In December, the team moved to their
new training complex in
Spata. The winter transfer window was disrupted by the free transfer of
Djebbour to Olympiacos, after a collision with the coach, while the team were strengthened by the loans of
Mateos from
Real Madrid and
Míchel from
Birmingham City, as well as the transfer of
Baha from
Málaga. The effort in the second half of the season was focused on the cup, as a result of which AEK suffering heavy defeats by
Olympiacos Volos with 0–4, a match for which suspicions were circulated about AEK football players being fixed, and by Olympiacos with 6–0. The 4–0 victory over
PAOK was not enough to make amends and at the end of regular period, AEK finished in 3rd place. In the play-offs, AEK started well in the first matches, but in the following games they faced hostile refereeing and the results were not as good. After the match at
Panthessaliko Stadium, the president of Olympiacos Volos, Achilleas Beos, who was punished, entered the teams' locker room. Thus, AEK filed an objection citing Beos' illegal entry into the field of play. The disciplinary committee of the league accepted the facts, but rejected the objection, considering that the locker room is not a playing field. In the last game, the indifferent AEK were defeated by Panathinaikos and finished 3rd in the play-offs. In the cup, AEK eliminated
Panthrakikos with an imposing 1–5 and then
AEL with 0–4 at their new stadium. The next opponent were Panathinaikos, who welcomed AEK to Olympic Stadium. Nikos Liberopoulos scored twice against his former club and AEK completely dominating the second half did not let their opponent react, with the final 0–2 showing that the qualification cas had been decided. In the rematch, at the side of AEK they expected an easy night to celebrate the qualification to the semi-finals of the institution, especially after the goal from
Lagos at the beginning of the match. However Panathinaikos did not give up, equalizing in the 21st minute with
Cissé and at the end of the half, they took the lead with
Gilberto Silva. Then, the greens continuing offensively, made it 1–3 with
Vyntra, getting a qualification score. The ultras of AEK, distraught, invaded the pitch, interrupting the game. With the restart, AEK pressed hard and in the 8th and last minute of stoppage time, won a foul in the center of the field. With all the players of the yellow-blacks, including the goalkeeper, at the opposite area, Míchel attempted something between a long cross and a shot and with
Karnezis out of position, he scored an incredible goal and gave AEK the qualification! In the semi-finals, AEK and PAOK faced each other with the first match at the Olympic Stadium finishing 0–0. In the rematch of the
Toumba Stadium, AEK imposed the game they wanted and at the beginning of the second half, they made it 0–1 with a header from Dellas. In the 59th minute, a flare from the gate of the ultras of PAOK hit
Saja, but the game continued as normal, until the 89th minute, when the ultras of PAOK invaded the field, chasing the players of AEK. The game was interrupted and the players of yellow-blacks eventually agreed to enter the pitch in order to finish the match formally and protect PAOK from severe punishment. Thus, AEK faced
Atromitos in the final at the Olympic Stadium. In the game, the yellow-blacks did not start well, but then they gained control with
Scocco as their main protagonist, where from a cross of his, Liberopoulos made it 0–1 with a header from an offside position. The game then became a stalemate, with Scocco leaving injured, but AEK managed to take the control of the match and score 2 more goals with Baha and
Kafes. From that point on, AEK ultras formed a cordon around the pitch and at a referee's whistle stormed in to celebrate with the game ending without all the minutes of stoppage time being played. This was followed by the inexplicable incidents caused by the ultras of AEK, who were forcefully trying to attack the fans of Atromitos, clashing with the riot police inside the stadium. ==Management team==