He had a strong spring campaign in 1993: after winning a stage in Paris–Nice and Dwars door Vlaanderen, he started as one of the favourites in the Tour of Flanders.

Museeuw won the Tour of Flanders in a two-man sprint with Frans Maassen, taking his first win in a monument classic.

He ended his spring campaign with a victory in the Amstel Gold Race after a two-man sprint with Italian Bruno Cenghialta, his fourth World Cup win.

In the Tour de France, he wore the yellow jersey again for three days, before losing it to Miguel Induráin in the long time trial to Bergerac.

His Mapei–GB team dominated the race and Museeuw arrived together with his Italian teammates Gianluca Bortolami and Andrea Tafi on the Roubaix Velodrome.

[13] In the summer he won his second Belgian national road race title, but again failed to win a stage in the Tour de France.

After a disappointing performance in Paris–Tours, where he wanted to secure his overall lead in the World Cup,[14] he stated he intended to quit cycling altogether.

He changed his mind and started the next week in the world championship road race, where he was not considered a favourite because of the mountainous course in Lugano.

To the surprise of many, and on his 31st birthday, Museeuw became world champion after a long breakaway with Mauro Gianetti, beating the Swiss in a two-man sprint.

[24] He fought back and resumed cycling after a long healing process, finishing third in the Tour of Flanders of 1999 and ninth in Paris–Roubaix, exactly one year after his horror crash.

[25] Upon crossing the finish line in victory, he lifted his left leg, pointing to his knee as a reminder of the injury that had almost ended his career two years before.

Towards the end of his career, he acted as a mentor to Tom Boonen, who was widely considered to be Museeuw's successor as leading figure in the cobbled classics.

In his last years as a professional he attempted to set a new record in the cobbled classics, aiming to win the Tour of Flanders or Paris–Roubaix a fourth time, but failed.

In his last classic race, the 2004 Paris–Roubaix, he punctured 5 km before the finish while riding in the leading breakaway, thereby losing his last chance of equalling Roger De Vlaeminck's record.

They recorded phone conversations between Museeuw and Landuyt speaking of wasps as a codeword for Aranesp, a synthetic hormone known to increase red blood cell levels.

On 24 January 2007, Museeuw confessed to the charges in a press conference, revealing that he had "not been completely honest in his last year as a professional, as he wanted to end his career in style", and announcing his resignation from his Quick Step team.

[31] In December 2008 Museeuw was convicted for doping offences by a Belgian Court, together with former cyclists Jo Planckaert and Chris Peers who were involved in the same affair.