Veyrat, who has received six Michelin stars in his career, was one of five top chefs at the COP21 meeting this month where leaders from across the globe sealed a deal to fight climate change.
He has been found guilty of environmental crimes after clearing 7,000 square metres (75,000 square feet) of protected forest in the mountainous Haute-Savoie region, to build a botanical garden, beehives and greenhouses next to his pricey restaurant La Maison des Bois.
The chef argued that he had good intentions and had created an educational site for children, but did not ask for authorization or get a building permit, according to the prosecution.
The building led to the destruction of "7,000 m2 of forest and the drying up of a wetland of nearly one hectare", according to the charges against him.
A French court ordered him to restore the wetlands within three months or face a fine of €3,000 every day past the deadline.
Veyrat was however found not guilty of a separate charge of contravening town planning laws.
"That allows Mr. Veyrat to keep his educational park for children with the botanical garden, greenhouses and apiary," said the chef's lawyer Nicolas Ballaloud.
He attributed the "heavy" fine to Veyrat's "fame"
During his court hearing Veyrat said he was "sorry for everything that has happened."
"I am not above the laws. Everyone can make mistakes, even me."
Known as much for roaming the countryside seeking wild herbs for his top-of-the-range dishes as for his trademark black hat, Veyrat has had several career setbacks.
In 2009, he stopped work, saying he could no longer bear the physical strains of the kitchen after a serious ski accident.
He handed back the six Michelin stars he had won (for two separate three-star restaurants) and only in 2013 re-entered the kitchen, opening his Alpine restaurant.
However a fire broke out at the wooden chalet restaurant in March this year, 1,800 metres up in the French Alps near the Swiss border.
Veyrat specializes in traditional dishes, with lots of wild herbs and "molecular gastronomy" – chemistry-inspired recipes that produce new textures such as emulsions in cuisine.
But such Michelin-starred genius does not come cheap.
According to his website, the top 12-course tasting menu at La Maison du Bois would set the diner back €325.