The Marion County Historical Society was founded in Salem on July 11, 1950, in an unsuccessful effort to save the building that housed Oregon’s first state legislature. The society’s main efforts during its first two decades were publishing and the preservation of historic buildings.

The society saved, among other buildings, the 1841 Salem Methodist parsonage and the former Thomas Kay Woolen Mills. In common cause with state archivist David Duniway, it also helped establish Mission Mill Museum, which features these structures. The society also periodically published Marion County History, the only periodical devoted to the county's history. 

In 1976, the Marion County Historical Society began to develop its own museum, and in April 1984 the museum moved into a former retail building on the Mission Mill grounds. With the help of several bequests, the society expanded its programming and publications in the 1990s. In 1998, it formed the Marion Historical Foundation as a supporting financial organization. By 1999, the American Association for State and Local History awarded the organization a certificate of commendation for outstanding local history efforts.

In 2002, at the request of the society’s board, Mission Mill staff operated the museum for a year while it planned for the future. In January 2010, after discussions about how the two organizations could reduce duplicative efforts and take advantage of complementary missions, the organizations merged and became the Willamette Heritage Center.