Benzonia was founded as an educational Christian colony on the model of Oberlin, Ohio in 1858 under the leadership of Charles Bailey. In 1860, the First Congregational Church of Benzonia was formed and organized in his home. Services were held in the Bailey home for two years before moving to the upper floor of the Grand Traverse College building as its place of worship.

It wasn’t until 1884 that construction of the church building foundation was started. Some years earlier, the lowering of Crystal Lake had exposed a wide beach on the north shore, strewn with sizable and accessible boulders. In the summer of 1883, the men of the church joined in a project to collect boulders to make the foundation of the proposed new church building. With the coming of winter snows, heavy sleighs, some drawn by oxen and others by horses, were dispatched to the north shore to bring the accumulation of boulders to the church site.

And so on July 24, 1884, the cornerstone of the foundation was laid. Work continued on the building through 1885 and 1886, and on December 7, 1886, the building was dedicated and used for the first time for a Sunday morning worship service. A new wing was added to the west side in 1913.

A new church building was begun in 1967 in the park to the north of the old building and was completed in 1968. The last church service in the old building was held in March of that year, and the building was formally decommissioned.  The decommissioned building was to become the Benzie Area Historical Museum. In January, 1969, the Congregational Church Board of Trustees negotiated a three-year lease with BAHS for use of the vacated church building, and BAHM first opened to the public on Memorial Day, 1969. After the first year of demonstrated ability, the church trustees presented a quit-claim deed to BAHS.

The decommissioned building was to become the Benzie Area Historical Museum. In January, 1969, the Congregational Church Board of Trustees negotiated a three-year lease with BAHS for use of the vacated church building, and BAHM first opened to the public on Memorial Day, 1969. After the first year of demonstrated ability, the church trustees presented a quit-claim deed to BAHS.

The grand opening of BAHS Museum was held on May 30, 1969, with over 200 people gathering before the old church, now the Museum, for the dedication. The ceremony opened with the Frankfort High School Band playing the National Anthem. Speakers included Allan Blacklock, Chairman of Benzie County Supervisors; Al Barnes, Traverse City area historian who gave the Dedicatory Address; and Rev William R. Catton, who gave a Dedicatory Prayer. Ray Antel, President of BAHS, and Dorothy B. Hensel, Museum Curator, gave remarks before the doors were opened for the first Museum guests to enter.

In celebration of Arbor Day on April 28, 1972, a memorial white pine tree, the Michigan State Tree was donated by Ellsworth Esch and planted by the Lake Shores Garden Club on the Museum grounds. Children from the fourth grade of Crystal Lake Elementary sang patriotic songs.

The Museum building received the State of Michigan Historic Site designation in April 1981.