Team captain George Hincapie crashed in a slippery section of the course leaving Boonen to ride for himself.

In 2005 Boonen won the Tour of Flanders, Paris–Roubaix and the E3 Prijs Vlaanderen, and came second in the Omloop "Het Volk" behind teammate Nick Nuyens.

Erik Dekker said: "I'm happy that I am near the end of my career, since with a cyclist like Boonen the spring classics will be rather boring the coming years".

[5] In Paris–Roubaix, Boonen entered the velodrome in the leading trio, and waited until the last moment before outsprinting George Hincapie and the Spaniard, Juan Antonio Flecha.

Leif Hoste, Peter Van Petegem and Vladimir Gusev placed second to fourth at Roubaix but were disqualified for riding through a closed level-crossing before a train passed.

Boonen abandoned the Tour during the 15th stage – 187 km from Gap to l'Alpe d'Huez – when he was unable to reach the summit of the Col du Lautaret.

Boonen won three stages of the Eneco Tour of Benelux but could not keep his title at the world championship, held on a circuit that was hillier than in Madrid 2005.

Boonen won stages 6 and 12 of the Tour de France in the absence of Alessandro Petacchi and Robbie McEwen.

In the Tour of Flanders he had to take on a defensive role when his teammate Stijn Devolder escaped and won for the second time.

On 27 April, Boonen tested positive for cocaine for the third time (the first, in November 2007, had not previously been made public).

After initiating legal proceedings he was allowed to compete in the Tour de France, just one day before the start on 3 July 2009.

He finished his season with a second place in Paris–Tours, beaten in a sprint of three by fellow countryman and defending champion Philippe Gilbert.

In February, he won the Tour of Qatar, winning two stages and the points classification, and finished second to Sep Vanmarcke in Omloop Het Nieuwsblad.

His third victory equalled those of Achiel Buysse, Fiorenzo Magni, Eric Leman and Johan Museeuw.

[22] Boonen won his first race of the year at the Heiste Pijl, an event not classified by the UCI,[23] then was the victor of the second stage of the Tour de Wallonie in July.

[24] The season started well for Boonen as he took the second place overall behind his teammate Niki Terpstra and the points classification jersey in the mostly flat Tour of Qatar.

At the 2015 Omloop Het Nieuwsblad Boonen made the decisive break with teammates Niki Terpstra and Stijn Vandenbergh, along with Ian Stannard (Team Sky).

[27] On 9 March Boonen crashed out of Paris–Nice, suffering a dislocated shoulder which ruled him out of the rest of the classics season.

[28] Boonen returned to racing in late April, at the Tour of Turkey, where his role was to lead-out his teammate Mark Cavendish.

[30] Boonen's season was brought to an end by a crash on the second stage of the Abu Dhabi Tour in October, which left him unconscious.

[31] After enduring a relatively quiet series of performances through most of the cobbled classics,[32] Boonen finished second at Paris–Roubaix, being pipped on the line by Mat Hayman.

[33] Despite not clinching the win, Boonen's aggressive performance in the race was acclaimed by former Paris–Roubaix champions Bernard Hinault and Gilbert Duclos-Lassalle, who described him as "a warrior" and "magnificent" respectively.

[41] He resumed his cobbled classics campaign at E3 Harelbeke, where he animated the race with an attack on the Taaienberg on his way to an eighth-place finish.

[42] He followed this up with a sixth place at Gent–Wevelgem, which he described as a satisfactory result, and a good indicator of form going into the cobbled Monuments.

[43] At the Tour of Flanders, Boonen had an eventful race: he led the Quick-Step squad into the foot of the Muur van Geraardsbergen, where he helped to force a breakaway group alongside team leader and eventual race winner Philippe Gilbert, and played a key part in enabling the group to distance the bunch.

[45] At his final race, Paris–Roubaix, Boonen finished 13th: after being part of the lead group with 35 km to go, he encouraged teammate Zdeněk Štybar to follow an attack by Daniel Oss, eventually enabling the Czech rider to finish the race as runner-up to Greg Van Avermaet.

[46] In February 2018 it was announced that Boonen had joined forces with Quick Step's long-time Belgian rivals, Lotto–Soudal, becoming a shareholder in the team and taking up the roles of technological adviser and ambassador for the team's Captains of Cycling supporters' programme, and linking up with his former agent Paul De Geyter, who had joined the squad as general manager in September 2017.

[49] The following month he made his car racing debut in the Volkswagen Beetle-based Fun Cup, competing in the 25 Hours of the VW Fun Cup at the Circuit de Spa-Francorchamps: he and team-mates Anthony Kumpen, Bert Longin and Ruben Van Gucht finished in 29th place out of 118 starters, 15 laps down on the winning team of Cédric Bollen, Fred Caprasse, Guillaume Mondron and Fred Bouvy.

He escaped major injuries during a crash at Assen that year after he collided with Kenneth Heyer at high speed.

[57] In 2016, Boonen paid back several million euros to the Belgian tax authorities for failing to declare his income while being a legal resident of Monaco.