ElBulli served its last supper and closed in July 2011, with Adria and business partner Juli Soler planning to establish "an experimental centre looking at the process of innovation and creativity."
Adria told The Associated Press the sale will raise funds for the foundation.
"In around a month's time, the full list of wines will be published," Adria said. "I don't really know that much about wine, I drink and enjoy them, but that's about as far as it goes."
He said many bottles were signed by producers and all would carry an elBulli Foundation identifying label.
Sotheby's auction house said in a statement that more than 8,800 bottles from elBulli's cellar would be auctioned with a view to raising an estimated $1.6 million.
El Bulli maintained an almost unattainable Michelin three-star status for over a decade and was rated the world's best restaurant five times by British magazine The Restaurant, with Adria often being cited as the world's most talented and imaginative chef.
In October, Soler, the maitre d' who discovered and signed up Adria, resigned from the elBulli Foundation after being diagnosed with a neuro-degenerative disease.
Since his arrival at El Bulli in 1981, Soler became an essential figure in what became one of the world's most influential restaurants.
Serena Sutcliffe, head of Sotheby's international wine department, said those lucky enough to have dined at elBulli will never forget the extraordinary sensations experienced there.
"There was surprise, delight and elation in every dish, a seamless procession of magic that opened up before one's eyes, only to disappear in a moment of bliss," she said.
Sutcliffe added that the food, which she described as all the secrets of smoke, foam and spheres of liquid involving melon to olives, was intuitively paired with "enticing and phenomenally interesting" wines.
The auctions, due to take place in Hong Kong on April 3 and New York on April 26, will offer connoisseurs an opportunity to buy a treasure trove, including continuous vintages of some of the world's most exclusive wines.
Examples include five vintages of Spain's Vega Sicilia "Unico," nine vintages of the rare Pingus and five vintages of Romanee Conti, the world's most sought-after red Burgundy.
Bordeaux wines, which many experts consider to be among the most collectable wines anywhere, are also present.
"All five First Growths are present in multiple vintages highlighted by full cases of bottles and magnums of Chateau Latour," the Sotheby's statement said.