Founder Duane Sorenson opened the first Stumptown cafe on Southeast Division Street in Portland in 1999, in a former beauty parlor. In 2003 the company began Direct Trade with the Aguirre family of Finca El Injerto in Guatemala, paying prices tied to cup quality, and it has worked with the Ketiara cooperative in Sumatra's Gayo Highlands since 2013.
Stumptown has roasted on Probat machines since the beginning, several of them refurbished vintage units. In New York it runs cafes in Greenwich Village, Brooklyn and the Ace Hotel.