After the 2006 FIFA World Cup, Japan's coach Zico became Fenerbahçe's new coach. Christoph Daum announced his retirement in the summer of 2006. After relegation in 2006, promotion to the top division followed again in 2007. Because the Turkish Football Association, due to the ongoing investigation, had limited access to the documents of the judiciary, it decided not (yet) to punish Fenerbahçe with a relegation. Because Arsenal's defense was so good, the national championship was immediately won in Dixon's first full season at the club. He already trained the club's second team between 1999 and 2002. He was fired on January 8, 2014, after Bologna failed to recover from relegation worries. The South American country won in the editions of 1958, 1962, 1970, 1978, 1986, 1994 and 2002. In 1990, 1998 and 2014, a European country won against a South American country in the final. At the end of 2002, all ten branches of the Swedish retail chain in the Netherlands were evacuated after bomb threats and the discovery of suspicious packages. At the end of August, UEFA gave the Turkish Federation an ultimatum: withdraw Fenerbahçe from the Champions League or risk a long suspension of Turkey and Turkish teams from international competitions.

Every year, at the end of September, the closing of "La Mercè" also takes place. The Dutchman Pierre van Hooijdonk was also recruited in that year. Pierre van Hooijdonk was second in the top scorers list. Napoli is the first club since the introduction of the UEFA Champions League to fail to qualify for the knockout phase with 12 points. The expectations came true and Fenerbahçe became champion again, this time with a difference of 3 points over number 2 Trabzonspor. Between Warrington and Flixton the channel joins the Mersey, and from there to Salford in that of the Irwell. The appearance of the temple is still somewhat known, because it is depicted on a relief of the Arch of Trajan in the Italian city of Benevento. This championship was celebrated twice because they became champions in the jubilee year (centennial) of arch-rival Galatasaray. The stadium was the first to be taken care of, because it was a major source of income and would become an even larger source of income for Fenerbahçe. At the start of the season, just before the transfer window closed, Fenerbahçe bought Mateja Kežman, Deivid de Souza and Brazil international Edu Dracena.

After a header from Lutsharel Geertruida in the final phase, according to the referee, just missed the back line, a cross from the same Geertruida was headed in by Dessers in stoppage time. This was and is a record; Fenerbahçe has still not lost with six goals in the Süper Lig to date. Aziz Yıldırım thought it was time for a stable team; this meant a coach who had to stay longer than six months, and a purchasing policy focused on the future. For the first time in history, Fenerbahçe became champion in the Süper Lig with a Turkish coach. No other Fenerbahçe player has been the top scorer of the Süper Lig with such a high number of goals. The club finished sixth in the Süper Lig. More and more well-known players also came to play football at the Istanbul club: Jay-Jay Okocha (left for Paris Saint-Germain), Elvir Baljić (left for Real Madrid CF), Emil Kostadinov (who came over from FC Bayern Munich), Jes Høgh ( left for Chelsea FC). More and more European famous players and trainers came to Istanbul to earn their living at Fenerbahçe. The white part, which also contains the name of the club (Fenerbahçe Spor Kulübü 1907), stands for purity and frankness.

The 2005/06 season was a season to forget for Fenerbahçe. This while Fenerbahçe won both home and away against the arch-rival in the competition, and also had eliminated Galatasaray in the Turkish Cup. Aziz Yıldırım wanted the stadium to become a place where one could come with the whole family, enjoy oneself and feel at home. Despite (or because of) the many changes, the new season did not start well: right in the first league match, Istanbulspor lost no less than 0-3 at home. It also meant that for the first time since 2013 the Champions League will not be won by a Spanish side. On March 6, 2019, Greenwood made his debut in the UEFA Champions League against Paris Saint-Germain (1-3 win). On April 16, 2011, Firmino scored his first goal in the Bundesliga against Eintracht Frankfurt, which was the only goal of the match.

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