Photo: Shake Shack Photo: Shake Shack Photo: Santiago Mejia / The Chronicle

Shake Shack, the hamburger chain founded by New York restaurateur Danny Meyer, has finally chosen a site in San Francisco: the former Real Food Co. market at 3060 Fillmore St. in Cow Hollow.

The natural-foods market, on the corner of Fillmore and Filbert streets, closed in 2016 after 19 years in business and has remained vacant since then. The owners of the building have filed an application to break up the 12,000-square-foot property into a fitness studio and restaurant, according to Shake Shack. SocketSite had previously reported on the plans.

“We are working with our real estate developer, Center Cal Properties, on the project,” Shake Shack spokeswoman Kristyn Clark confirmed, adding that both parties are in the early stages of getting the appropriate approvals.

As The Chronicle reported in January, Shake Shack, which has more than 160 locations worldwide, plans to open its first two Bay Area restaurants in Palo Alto’s Stanford Shopping Center and the Marin Country Mart in Larkspur in the fall. San Francisco will be its third.

Shake Shack CEO Randy Garutti told The Chronicle in January that the Marina neighborhood, adjacent to Cow Hollow, was a good possibility for a San Francisco location because of its reputation as a “community gathering space.” The neighborhood also tends to be slightly more friendly toward chains than, say, the Mission or the Haight.

Shake Shack will be competing with the locally owned Super Duper Burger and Roam Burgers, both of which have locations less than a half-mile away. Neither, however, serves crinkle-cut fries.

Jonathan Kauffman is a San Francisco Chronicle staff writer. Email: jkauffman@sfchronicle.com Twitter: jonkauffman