The fire was reported at the bakery, located at 6528 Washington St., at about 4:30 a.m., said Capt. Jim Christison of the Napa County Fire Department's Yountville station.
The fire burned a 100- to 150-square-foot area of the roof over an oven and was controlled in 20 minutes, Christison said.
Three employees were working in the bakery at the time, and no injuries were reported, Christison said. The cause of the fire has not been determined.
Approximately 30 firefighters from Napa County fire and Cal Fire responded to the blaze, Christison said.
Keller also owns the famous French Laundry restaurant in Yountville. He opened the Bouchon Bakery in 2003, and has eight restaurants and two bakeries in the United States, according to the Bouchon Bakery's website.