The Waggoners were early millers in Perry and Cumberland Counties, Pennsylvania.  In 1865, Peter Waggoner, Sr. sent his son William to Independence to look over business opportunities.  William liked the prospects, and in 1867 the family purchased the "old City mill" from John Overfelt.  The family business developed a reputation for producing the very best in baking and cake flours, and "Queen of the Pantry" flours became known all over the middle west. 

Reflecting their improved economic condition, the Waggoner's new home across the street from their rapidly growing flour mill immediately began to be adjusted to fit the needs and expectations of its owners.  During the 1890's, extensive renovation was done to the home when William Henry, Jr. and his wife moved into the home.  They contracted the architectural firm of Root and Siemens, with Mr. Henry Ohaus in charge of interior decoration. 

The Waggoner family continued to live in this home until 1976, when Harry K. Waggoner died.  In 1979, a group of private citizens, in cooperation with the City of Independence, purchased the 19.5-acre tract for a museum and public park.