In 1800 Lozeno Dow, a circuit rider, held a rally at a field by Route 100, which marked the beginning of the Methodist group in Waterbury. For many years the group met at private residences in the area, including in a barn on the farm of Captain Lemuel Lyon. The timbers of the barn were used to frame the present Waterbury Center Community Church. The original church began construction in the early 1830's and was built of brick with slabs of native stone for the underpinning, many paned windows, and no basement. The interior was a single large room with a gallery running around three sides, and the pews were of the old "box" type with doors that buttoned shut and faced the front door. Dedicated in 1832 as a Methodist Episcopal Church in the Vermont conference, the building was finally completed in 1833. In 1857, Lyon drove with an ox team to Boston to retrieve the church bell.

In April 1858, Lyon deeded the parsonage to the trustees (it was ultimately sold in 1976). Also in 1858, the church was remodeled, removing the side galleries to add a second floor and installing the current pews. The finish on them has never been touched. Later, the lower part of the church was divided by semi-movable partitions using boards from the old pews, and a kitchen was added. Mrs. Mirancy Hopkins presented memorial windows in 1894 in memory of her parents, Mr. and Mrs. Lemuel Lyon. The windows commemorate the names of early pillars of the church.

The first church wedding was held in 1850 when Albert Lyon and Matilda Jones were married by Reverend Hawley Ransom. In 1919 the local Baptist and Methodist churches merged, with summer services being held at the Baptist Church and winter services being held at the Methodist Church until 1928, when the Baptist church was sold to the Grange. In 1963, the Waterbury Center Community Church became incorporated. In 1978, it was designated as a Vermont and National Historic Place.