Whole Foods Market will open its largest Hawaii store by early summer in Kakaako after a dozen years of planning and setbacks.

The health food giant that specializes in organic and natural products will begin operations at its fourth Hawaii location by June, the company said Monday.

The latest Whole Foods will occupy the first two floors at the $429 million Ae‘o condominium at 1001 Queen St., part of the master-planned community of Ward Village.

The 72,000-square-foot, two-story store will be more than twice the size of its second-largest Hawaii store in Kailua. The new store will sell locally grown products — including produce, seafood and meats — as well as its popular natural body items, and will offer indoor and outdoor seating.

“We are thrilled to be opening our third store on Oahu and to serve as a new gathering place for the local community,” said Marci Frumkin, a company spokeswoman, in an emailed statement.

The company would not say how many employees it will be hiring or give an exact opening date. It also didn’t disclose future expansion plans for the islands.

Whole Foods first announced its plans to open a Kakaako flagship store in 2006, as the anchor tenant at the site now occupied by TJ Maxx. The Austin, Texas-based retailer planned to open the store in early 2008, but walked away from the project after delays caused by the discovery of iwi, or Native Hawaiian remains, followed by the recession and later the bankruptcy of former developer General Growth Properties.

The new location, on the site of the former Office Depot and Nordstrom Rack, will be blocks away from local natural foods retailer Down to Earth, which is scheduled to open a 13,000-square-foot store in early April on the ground floor of Keauhou Lane, a new mid-rise apartment building at the corner of Keawe and Pohukaina streets.

Whole Foods first entered Hawaii in 2008 with its Kahala Mall store, which is just over 28,000 square feet. That was followed in 2010 by a 27,000-square-foot store in Kahului and a 32,000-square-foot Kailua outlet, which opened in 2012.

The store is part of Dallas-based Howard Hughes’ $7.5 billion master plan calling for 16 towers with as many as 4,300 residential units and 1 million square feet of retail space at the 60-acre Ward Village.