Returned back to Turkey after one season, he was responsible for Galatasaray again. The team won Turkish Cup under his management in 1991-1992 and played in the quarter finals of the Cup Winners Cup. From 1992 to 1995, he coached Kocaelispor and then he was appointed the second time head coach for the national team, he served until 2000. At the 2000 European Football Championship, Turkey played quarter finals with him, first time ever in the country’s history.

In 2000, Fenerbahçe offered him a position, and at the end of the season 2000-2001, Fenerbahçe won the league championship title after 5 years again. Denizli is the first Turkish coach of Fenerbahçe ever to win the league championship, but he enjoyed a rather poor Champions League run with defeats against FC Barcelona and Bayer Leverkusen. In 2002 the Nigerian national football team wanted to sign Denizli for their 2002 World Cup campaign but due to several problems it was canceld. He then transferred to Vestel Manisaspor.

In 2004, Denizli received several offers from Japan and South-Korea, but he chose to use his knowledge for Iran to coach the premier league champion Pas Tehran. Denizli made a run for the league title but became only second in the league. There were rumours that Denizli would be the coach of the Iran national football team to lead it to a successful 2006 World Cup. He also reached the quarterfinals of the AFC Champions League with Pas, where he was knocked out 4-4 on aggregate by Al Ain. Denizli said he was going to leave Pas and headback for Turkey, although he had an option to sign a contract in Dubai. It was said that Mustafa Denizli would take over the Iranian national team after Branko Ivankovic failed to make an impression on the world stage, but the Iranian Amir Ghalenoei was chosen over him. In August 2006, Denizli was hired as the manager of the Iranian club, Persepolis FC, after Arie Haan was fired.