In 1895, Jones opened a store at 6th and Main in the River Market neighborhood of Kansas City, Missouri.

In 1902 Jones leased a 500,000-square-foot (46,000 m2) seven-story building that took up an entire block at 12th Street and Main across the street from Bernheimer Bros. & Co. Jones declared bankruptcy in 1910 and the store was taken over by New York interests.

It was acquired by May Department Stores in 1998 after the Dillard's acquisition of Mercantile, and integrated into the company's Famous-Barr division.

On February 1, 2006, The Jones Store Co. was assumed by the new Macy's Midwest division of Federated.

On September 9, 2006, The Jones Store Co. name was phased out in favor of the Macy's nameplate, marking the second entry for Macy's into Kansas City and Topeka ever since the chain sold its original Kansas City stores to Dillard's in 1985.