The first Stone & Thomas Department Store opened in 1847 on Market Street in Wheeling, as the Bee Hive. It was owned by Jacob C. Thomas and Elijah J. Stone, who later married Thomas's sister. Renamed Stone & Thomas, the store and the company prospered for well over a century. Owned and operated by the same family for five generations, Stone & Thomas grew to become West Virginia's largest independent retailer and one of the top 75 independent retail store chains in the country.

After World War II, major expansion began under Wilbur Stone Jones, great-grandson of the founder, by acquiring stores and building new stores. In the next generation, Stone & Thomas became one of the largest family-owned department store chains in the country, under the joint leadership of Wilbur Stone Jones, Jr., and Edward C. Armbrecht, Jr., his brother-in-law.

By the late 20th century, Stone & Thomas had expanded its flagship store in Wheeling to 182,000 square feet. The chain entered the Charleston market in 1941, and in 1948 opened a fine new store in the heart of downtown. At its peak Stone & Thomas had 21 stores in West Virginia, Ohio, Kentucky, and Virginia, with more than 2,000 employees. It met the needs of generations of shoppers with broad assortments in apparel and home furnishings.

Stone & Thomas closed its landmark Charleston store as the city's shopping habits changed. In 1998 Stone & Thomas was sold to the Elder-Beerman Company of Dayton, Ohio. Elder-Beerman renamed the stores, and the familiar Stone & Thomas name disappeared from the region's commercial landscape.