The veteran, who has raced nine Tours de France, recently rode the Critérium du Dauphiné and told his Lotto-Dstny team that he doesn't feel ready to take on the Tour next month. Instead, he'll ride from Semmerzake to Calpe as he prepares to race the ninth Vuelta of his career.
Speaking to Sporza after the conclusion of the Dauphiné, Lotto directeur sportif Kurt Van de Wouwer said that De Gendt informed him of the decision on Sunday evening after leaving the race.
"I wasn't shocked by that phone call. I felt it coming," Van de Wouwer said. "It's a logical consequence of everything Thomas has already encountered this season. At the Tour, we need a De Gendt who is 100%, and at the moment he is not."
De Gendt has two Tour de France stage wins, five stage combativity awards, and a spell in the polka dot jersey on his palmarès but he's not set to add to those achievements this July.
He will be riding through France though, heading south from Flanders towards the popular winter training location of Calpe in southeast Spain, with a stop in Andorra along the way.
Writing on Twitter on Monday, De Gendt said, "Any volunteers to tag along somewhere? Feel free to join in." The big trip will see him work towards the Vuelta, where he won a stage to Gijón in 2017 and won the mountain classification a year later.
It's an unconventional way to prepare for a Grand Tour, but his team trust a rider who has started 23 of them to get into shape ahead of another three-week test.
"He is now aiming for the Vuelta," said Van de Wouwer. "Thomas, with all his experience, knows well enough what he needs to do to be ready for the Vuelta, his next goal. He has to go for that now."
The Dauphiné was his first race since the Boucles de Mayenne at the end of May. De Gendt made the break on stage 5 to Salins-les-Bains before the move was caught on the final climb of the day 17km out.
He was joined at the race by teammate Victor Campenaerts, who was in action for the first time since fracturing a vertebra at the Bredene Koksijde Classic back in mid-March.
The former Hour Record holder wore the polka dot mountains jersey on stage 7 before losing it to stage 8 breakaway and winner Giulio Ciccone (Trek-Segafredo). His progress is encouraging, Van de Wouwer said, and he'll have a chance of making the team's Tour de France squad.
"Victor surprised us," he said. "When a rider has been out of competition, it's always a question of how far away he is. But it is clear that he is ahead of his original schedule.
"In the Dauphiné, Victor gave more than a 'calling card'. But I won't make any statements about the [Tour] selection right now. Next Monday we will sit together and make the decisions."
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Daniel Ostanek is production editor at Cyclingnews, having joined in 2017 as a freelance contributor and later being hired as staff writer. Prior to joining the team, he had written for most major publications in the cycling world, including CyclingWeekly, Rouleur, and CyclingTips.
Daniel has reported from the world's top races, including the Tour de France and the spring Classics, and has interviewed many of the sport's biggest stars, including Wout van Aert, Remco Evenepoel, Demi Vollering, and Anna van der Breggen.
As well as original reporting, news and feature writing, and production work, Daniel also runs The Leadout newsletter and oversees How to Watch guides throughout the season. His favourite races are Strade Bianche and the Volta a Portugal, and he rides a Colnago C40.