The first mill was built in 1830 by John A. Overfelt about a block north of the second mill's location near a spring which was the source of power. The Waggoners were millers from Perry and Cumberland Counties in Pennsylvania. Peter Waggoner bought the "old city mill" from Overfelt in 1867, operated it until he retired, then passed it on to his son who had been milling with him at the mill.

William rebuilt the mill a block south, expanded it, and changed it from a merchant grist mill into a flour mill in 1875, the same year that he partnered with George Porterfield Gates to establish the Waggoner & Gates Mill. Gates was the maternal grandfather of Bess Wallace Truman, wife of Harry S. Truman, former President of the United Sates. In 1883, the enterprise became known as the Waggoner-Gates Milling Co.

The mill was a regional mill that enjoyed a national sales. In 1903, the mill had a capacity for 1000 barrels/day, which was later expanded to 13,000 barrels/day. A grain elevator along the RR tracks by the mill was expaneded from 75,000 bushels to 350,000 bushels capacity through the early to mid. 1900's. Flours produced were: Jack Frost Flour, Famous Brand Flour, N.B.C. Special Strong Bleached Flour, and the most popular-Queen of the Pantry Flour. The Oct. 11, 1940 Independence Examiner disclosed that the mill regularly employed about 60 men at the modern, electrically operated mill. The water tower still overlooks the old mill structure.

The mill ceased production after the end of World War II, finally closing in 1957. The milling complex was reduced to a large heap of rubble in 1967 following an explosion and fire. In 1989, the long, 2 story brick storage structure that remained following the fire, was converted into the National Frontier TRails Center, commenorating all the trails west, many of which originated from Independence or nearby St. Joseph, Mo. The Oregon TRail, The Santa Fe Trail, the California Trail, and Lewis & Clarks Corp of Discovery Trail are all featured in exhibits at the museum. See the above website and click on history of mill for a photo of the original 1875 mill complex. The long building on the lower right is the current Trails Center. *Update: The fully restored Chicago-Alton Depot which was moved to it's current location behind the Frontier Trails Museum (aka Waggoner-Gates Mill). The depot was originally located about a half-mile southwest of the mill. Rick Webb April 2008*