In this decade, a strong side was created with players from the late 1950s and new important players, such as Giannis Gaitatzis, Nikos Gioutsos, Pavlos Vasileiou, Vasilis Botinos, Giannis Fronimidis, Christos Zanteroglou, Grigoris Aganian, Stathis Tsanaktsis, Mimis Plessas, Giangos Simantiris, Pavlos Grigoriadis, Savvas Papazoglou, Stelios Besis, Sotiris Gavetsos, Tasos Sourounis, Vangelis Milisis, Orestis Pavlidis, Panagiotis Barbalias and last but not least the prolific goalscorer Giorgos Sideris, top-scorer in the club's history with 493 goals in 519 matches in all competitions (224 goals in 284 Greek Championship matches).

[47] Bukovi's innovatory tactics and groundbreaking training methods transformed Olympiacos and created a powerful, attacking team with constant player movement and solid combination game that often played spectacular football.

[51] They won the title in a convincing way and with some notable wins, like the 4–0 smashing victory against arch-rivals Panathinaikos at the Karaiskakis Stadium (Vasileiou 17', Sideris 20', 35', 62'), where Olympiacos played spectacular football and missed a plethora of chances for a much bigger score.

[54] Furthermore, the regime cancelled the transfer of Giorgos Koudas to Olympiacos[55] and days later another blow was delivered to the club: Márton Bukovi, already a legend and architect of the great 1965–67 team, was forced out of Greece by the military junta, being labelled a communist.

[59] He appointed Lakis Petropoulos as head coach and signed top-class players, creating a great roster with key performers such as Giorgos Delikaris, Yves Triantafyllos, Julio Losada, Milton Viera, Panagiotis Kelesidis, Michalis Kritikopoulos, Takis Synetopoulos, Romain Argyroudis, Maik Galakos, Nikos Gioutsos, Giannis Gaitatzis, Vasilis Siokos, Thanasis Angelis, Lakis Glezos, Petros Karavitis, Kostas Davourlis, Giannis Kyrastas, Dimitris Persidis, Lefteris Poupakis and Babis Stavropoulos.

[3] On the pitch, the team, with all the financial and managerial problems, as well as the lack of strong administrative leadership until the Kokkalis arrival, spent nine seasons without a league title, from 1988 to 1996, despite the foreign top-class players that played for the club at that period, such as Lajos Détári, Oleh Protasov, Juan Gilberto Funes, Bent Christensen, Hennadiy Lytovchenko, Yuri Savichev, Andrzej Juskowiak, Daniel Batista, Fabián Estay and the backbone of solid Greek players like Vassilis Karapialis, Kiriakos Karataidis, Giotis Tsalouchidis, Nikos Tsiantakis, Giorgos Vaitsis, Minas Hantzidis, Theodoros Pahatouridis, Savvas Kofidis, Chris Kalantzis, Gιorgοs Mitsibonas, Ilias Talikriadis, Alekos Rantos, Panagiotis Sofianopoulos, Ilias Savvidis and Michalis Vlachos.

[3] By that time, Olympiacos had already a very strong roster, with players like Kyriakos Karataidis, Vassilis Karapialis, Grigoris Georgatos, Alexis Alexandris, Giorgos Amanatidis, Nikos Dabizas and Ilija Ivić.

He purchased the highly rated prospects Predrag Đorđević and Stelios Giannakopoulos from Paniliakos, outbidding both AEK Athens and Panathinaikos; signed Refik Šabanadžović, Andreas Niniadis, Giorgos Anatolakis and Alekos Kaklamanos; and brought Olympiacos Academy product Dimitris Eleftheropoulos back from his loan spell at Proodeftiki.

In the second leg in Athens, Olympiacos totally dominated the match, and scored the goal that put them in the driving seat in the 12th minute of the game, when Siniša Gogić's powerful header found the back of the net after Grigoris Georgatos's superb cross.

[77] Despite the big disappointment from the way the qualification to the semi-finals was lost, the presence of the team in the Champions League quarter-finals, one of their best European campaigns, combined with the domestic double, marked a very successful season for the club, arguably the best in their long history.

These transfers strengthened even more the already strong roster from the previous successful years and under the guidance of coaches like Giannis Matzourakis, Takis Lemonis and Oleg Protasov (Bajević had left the club in 1999), Olympiacos managed to win seven consecutive Greek Championships (1997–2003), breaking their own past record of six (1954–1959).

[78] Olympiacos beat Panathinaikos 3–0 (Giovanni 3', Giannakopoulos 15' 48') in a dominant display in Rizoupoli[78] and celebrated the all-time record of seven straight Championships, which was a dream and a historic objective for the club and especially for the fans.

[85] However, the team's less than satisfactory performance in the league, coupled with the defeat from Chelsea in Stamford Bridge for the knockout phase, prompted club owner Sokratis Kokkalis to sack coach Takis Lemonis.

In the summer of 2008, Olympiacos made prominent transfers, signing Dudu Cearense, Avraam Papadopoulos, Diogo Luis Santo and Matt Derbyshire and appointed Ernesto Valverde as the new coach with a three-year contract worth approximately €6 million.

Olympiacos appointed former Brazil legend Zico as their coach and started the 2009–10 season with great success, as they qualified for the Champions League final 16, finishing second in Group H only 3 points behind Arsenal,[88] despite the absence of numerous first-team players due to injuries.

[3] During the first year of his presidency, Marinakis appointed fans' favourite Ernesto Valverde as coach (who came back for a second tenure in the club) and signed players with international pedigree, such as Albert Riera, Ariel Ibagaza, Kevin Mirallas, Marko Pantelić and François Modesto.

[3] The expectations for the 2013–14 season were very high, especially after the signing of players such as striker Javier Saviola, Joel Campbell, Roberto, Alejandro Domínguez, Vladimír Weiss, Delvin N'Dinga and Leandro Salino.

[3] Despite the two-goal advantage which put them within touching distance of a quarter-final place for the first time since 1999, Olympiacos lost 3–0 in the second leg in Old Trafford, having missed an outstanding double chance to equalise the score in the 40th minute.

In the 2014–15 season, Olympiacos entered the 2014–15 Champions League group stage with hopes to repeat the previous year's performance; they were drawn alongside Atlético Madrid, Juventus and Malmö FF.

[94] Domestically, Olympiacos had perhaps their most successful season in years, as the team managed to secure their 43rd Greek Championship, and 6th consecutive, on the last day of February 2016, considered a national record for the earliest time, within a league campaign, when a title is clinched.

At the start of the 2017–18 season, the board decided to hire former Anderlecht manager Besnik Hasi to guide Olympiacos back to the UEFA Champions League group stage after a year's absence.

Upon his arrival, Hasi strengthened the squad with players as Vadis Odjidja-Ofoe, Guillaume Gillet, Mehdi Carcela, Jagoš Vuković, Björn Engels, Uroš Đurđević, Emmanuel Emenike and Panagiotis Tachtsidis.

Aggregate victories over Partizan (5–3) and Rijeka (3–1) in the two final qualifying rounds ensured the Red-Whites' presence in Group D of the competition, considered perhaps the toughest in Olympiacos' European history due to Barcelona, Juventus and Sporting CP being the opponents.

[101] Despite being in the Super League lead halfway through the season, Lemonis was dismissed on grounds of dressing room instability, and Óscar García was subsequently appointed with a vision of increasing attacking efficiency and discipline.

In the Super League the Red-Whites conceded the title to AEK three matchdays before completion, thus ending a run of seven consecutive championship wins and leading to the dismissal of García after two months at the club's helm, with Christos Kontis finishing the season as caretaker manager.

Beginning in the Europa League third qualifying round, the club ensured a group stage participation for the third season in a row, after knocking out Belgian KRC Genk and Serbian rookies FK Čukarički.

After knocking out Hungarian champion Ferencváros in the play-offs with 2 Ayoub El Kaabi goals, they faced Israeli Maccabi Tel Aviv in the Round of 16, and got stunned by a 1–4 defeat at Karaiskakis Stadium.

With everything looking like the tie would be settled on penalties, a 116th minute cross by Santiago Hezze landed on El Kaabi's head, who put the ball in Terracciano's net to make it 1–0, causing delirium among millions of Olympiacos fans all over the world.

After a VAR check by Artur Soares Dias, the goal was confirmed and the game ended in that score, with Olympiacos making history and becoming the only Greek football club to win a UEFA competition.

Olympiacos has eliminated (in either finals, knockout matches or group stages) clubs like Milan, Arsenal, Ajax, Benfica, Porto, Borussia Dortmund, Lazio, Celtic, PSV Eindhoven, Aston Villa, Werder Bremen, Fiorentina, Anderlecht, Monaco, Deportivo La Coruña, Hertha BSC, Cagliari and Standard Liège among many others.