The Michelin Guide for Spain and Portugal 2014 has DiverXO as the country's eighth three-star restaurant.
DiverXO has built up a very strong reputation with its combination of European and Asian flavours since it opened in its new premises in 2009.
"I'm amazingly happy," the restaurants's 33-year-old chef told Spain's El Mundo newspaper on Wednesday.
"It's been a huge effort to get (the restaurant) up and running," said Muñoz, who added he was grateful to all the people who had helped.
The young chef expressed his surprise at the meteoric rise of DiverXO given its small size. Being awarded a third Michelin star was like joining (football's) Champions League, he said.
The new Michelin guide also lists a pair of new two-star Michelin restaurants: El Portal de Echaurren in La Rioja and M.B. by chef Martin Berasategui in Tenerife.
Among the restaurants to earn a first star was the Barcelona run Tickets, run by the star chefs Ferran Adrià and his brother Albert, who were behind the now-closed elBulli restaurant.