On 4 October 2013, a day after the home defeat to Eintracht Frankfurt in the group stage of the UEFA Europa League, the club announced the termination of Paulo Sérgio's contract, due to a disappointing run of results domestically and abroad.
On 7 October 2013, APOEL won Aris Limassol 1–0 at home under caretaker coach Yiannos Ioannou, with Nuno Morais scoring the only goal of the match in the 13th minute.
Henrique scored the first goal for Ermis in the 81st minute by illegally using his right hand and the same player made it 2–0 from a penalty kick in the injury time.
On 2 November 2013, APOEL's disappointing run continued as the champions were defeated 0–2 by Apollon Limassol at Tsirion Stadium, thanks to Fotios Papoulis and Marcos Gullón second half goals.
Esmaël Gonçalves scored a hat-trick, while Gustavo Manduca and Constantinos Charalambides added a goal apiece in APOEL's victory.
On 22 December 2013, APOEL sealed their fourth consecutive league win by beating Enosis Neon Paralimni 3–0 at Tasos Markou Stadium.
On 11 January 2014, APOEL drew their second league game in a row as they were held 1–1 by AEK Larnaca at GSZ Stadium and dropped to the 4th place, six points behind leaders AEL Limassol.
On 5 February 2014, APOEL continued their impressive form with a well deserved 2–1 win over Anorthosis at Antonis Papadopoulos Stadium and coupled with the unexpected draw of leaders AEL Limassol closed the gap at the top to four points.
Efstathios Aloneftis notched a hat-trick and Brazilian forward Gustavo Manduca scored the other two, while Doxa's consolation goal came from a powerful 40-yard shot from Nilson Antonio.
Within 25 minutes the game was all but over as a brace from Tomás De Vincenti, a Gustavo Manduca penalty and a red card for AEK Kouklia's Pantelis Pitsillos gave APOEL a 3–0 lead.
AEK Kouklia managed to reduce the deficit through Alexandros Garpozis before the break but APOEL proved too strong as Nektarios Alexandrou and substitute César Santin with a couple completed the rout.
On 19 March 2014, APOEL were held to a goalless draw by Omonia at GSP Stadium and dropped to the third place, three points behind leaders AEL Limassol.
On 23 March 2014, in its first Championship play-off match, APOEL maintained the pressure on AEL Limassol with a slender 2–1 win over Ermis Aradippou at Ammochostos Stadium.
On 5 April 2014, APOEL were held to a goalless draw by Omonia at GSP Stadium and remained three points behind leaders AEL Limassol, which they also drew against Apollon.
APOEL got off to a great start when Efstathios Aloneftis crossed the ball and Nuno Morais headed past AEL keeper Karim Fegrouche in the fifth minute.
Four minutes before half time Tiago Gomes released Constantinos Charalambides on the right side and his cross was headed past Fegrouche by César Santin.
The icing on the cake came late on in the game when APOEL's midfielder Nuno Morais ran clear and set Gustavo Manduca up for an easy third goal.
Tomás De Vincenti grabbed a hat-trick, Kaká a brace with João Guilherme, Cillian Sheridan and Mário Sérgio also getting on the scoreboard, while Nuno Morais put the ball into his own net to score Anorthosis' only goal.
Unfortunately, the referee suspended the match just six minutes into the second half (when the score was still at 0–0), when firecrackers thrown by AEL fans, hit and injured APOEL's Brazilian defender Kaká, who was put on stretchers and rushed to hospital.
APOEL, who needed to win their league-deciding replay in order to pip AEL's charges on head-to-head record, scored through Cillian Sheridan on the brink of half-time and won their second consecutive league title, in one of the most hotly contested championships in recent years.
On 8 January 2014, in the first leg of their Cypriot Cup second round clash, APOEL secured a narrow 1–0 advantage over AEL Limassol at GSP Stadium after Irish striker Cillian Sheridan scored from close range in the 40th minute.
On 22 January 2014, APOEL recorded another 1–0 win over AEL Limassol at Tsirion Stadium for an aggregate 2–0 victory over last season's beaten finalists in the second round of the Cypriot Cup.
On 19 February 2014, APOEL easily beat Alki Larnaca 3–0 at GSP Stadium and qualified for the Cypriot Cup semi-finals for the first time in four years.
On 2 April 2014, in first leg semi-final tie, APOEL all but booked their place in the final with a resounding 4–1 home win over Doxa Katokopias.
On 9 April 2014, despite fielding a team based only on reserve players, APOEL easily beat Doxa Katokopias 4–0 at Makario Stadium and reached the Cup final, with Christos Pipinis, a brace from Aldo Adorno and César Santin getting the goals.
[10][11] The club had not won the trophy since the 2007–08 season but the first half goals from Tomás De Vincenti and Cillian Sheridan ensured that the cup would be going back to APOEL after a six-year absence.
In the second leg, APOEL took the initiative from the first whistle and maintained a 60% ball possession at Ljudski vrt, but they only managed a goalless draw against Maribor and were eliminated on away goals rule after a 1–1 aggregate score.
Despite losing to Zulte Waregem in the play-off round, APOEL reinstated in Europa League, replacing the Turkish side Fenerbahçe who were banned because of the match-fixing case related to the 2010–11 Süper Lig title.
Note: Despite losing to Zulte Waregem in the play-off round, APOEL reinstated in Europa League replacing the Turkish side Fenerbahçe who were banned because of the match-fixing case related to the 2010–11 Süper Lig title.