The Shaker Museum | Mount Lebanon was founded in 1950 by John S. Williams, Sr. on the site of his Old Chatham farm in Columbia County, New York, in collaboration with the Shaker leadership then extant at Canterbury Shaker Village, NH,  Sabbathday Lake, ME, and Hancock Shaker Village, MA.

The Shaker Museum was the first and, at that time, only public museum dedicated to preserving the life, work, art and religious history of the United Society of Believers in Christ's Second Appearing, commonly known as the Shakers.

The important artifacts that the Shakers made available to the Shaker Museum and Library reflect the role they expected the institution to play in the preservation of their history. Between 1950 and 1962, 70 percent of the collection was acquired. The capstone of the initial collecting effort was the accumulation of journals, printed material, manuscripts, and photographs in the care of the Central Ministry that were presented to the Shaker Museum and Library in 1962 by Eldress Emma B. King.

The Shaker Museum and Library has built a reputation as the premier study collection of Shaker life, culture and religion and as an essential resource for scholars and researchers. The Museum was first accredited by the American Association of Museums (AAM) in 1972. Upon the founder's death in 1982, the institution evolved from a family-based collection to a professional institution. In 1990, the Board of Directors changed the organization's name to the Shaker Museum and Library, in recognition of the dual nature of the institution's collections.

In 2001, the Shaker Museum and Library received a Save America's Treasures grant to investigate the feasibility of acquiring the North Family at Mount Lebanon Shaker Village in New Lebanon, New York, a National Historic Landmark; restoring the site for public benefit; and relocating the museum and library to a new state-of-the-art facility at that location. The resulting Master Plan for the site, prepared by a team under the leadership of Cooper, Robertson and Partners of New York City, included Historic Structures Reports for the buildings, a Cultural Landscape Report, and prioritized plans for restoration of the site.

The Museum Board of Trustees approved the strategy of relocating the Museum to Mount Lebanon, and, in 2004, the Museum acquired the site, consisting of 30 acres and 10 extant Shaker buildings, plus the iconic Mount Lebanon Meetinghouse, which is leased to the adjacent Darrow School as its campus library facility. In 2004, and again in 2006, the World Monuments Fund recognized the site on its list of the 100 most significant endangered historic sites in the world.

The Museum began restorations at the site in 2005, beginning with emergency stabilization of the 1854 Wash House. Summer field schools held at the site in 2006 and 2007 complemented the restoration effort. Restoration efforts will continue in 2009 on the Granary and Brethren’s Workshop buildings, and in 2010 construction is scheduled for the restorations of the Wash House and stabilization of the masonry walls of the Great Stone Barn.

In early 2009, in line with the Museum’s goal to move to Mount Lebanon, the Board of Trustees approved to close the museum galleries in Old Chatham to the public; to prepare the collection for its eventual relocation; and to move public programs and events to Mount Lebanon. In 2012, the Museum officially became the Shaker Museum | Mount Lebanon.

Beginning in 2013, the Museum has undertaken a multimillion dollar project to stabilize and partially reconstruct the massive remains of the Great Stone Barn. September 2014 saw the completion of the first phase of the project which promises to allow public visitors limited access to the Barn as a part of its interpretive tours of the North Family. The North Pastures, which formed the Family's stone-walled fields, sit on 61 acres of land adjacent to the historic site and were purchased by the Museum in the spring of 2014, bringing the total acreage of the North Family to 91. A walking loop trail has been opened up for public use.