The Lyndon Free Baptists¹ were the first denominational group organized in Lyndon, in 1802. Little is known of the activities of this group. It wasn't until 1816 that Daniel Quimby built a church on Pudding Hill. Again, little is known of this church, but there are records of itinerant ministers speaking of "Brother Quimby's church."

In 1840, the Methodists vacated the Meeting House in Lyndon Center, and the Free Baptists consolidated their worship in that place. In 1843 a new church was formally organized by its first pastor, Rev. T. P. Moulton, with nine members, and a church building erected facing west on Main Street, as well as a parsonage where Lyndon Institute's main building now stands. Before the Lyndon Literary and Biblical Institute (Lyndon Institute's predecessor) erected Thompson Hall in 1869, the parsonage was moved to Main Street, where it still stands.

In 1872 the church building was moved from Main Street to what is now known as College Road, turned to

face north, a vestry added under it, a vestibule and steeple added to the front, and horse sheds erected behind it. This work was finally finished in 1874.

In 1902 the church building was extensively renovated, both the inside and the outside receiving some much-needed attention. Shortly after, in 1906, an indoor baptistry was installed under the speaker's platform, and in 1913, after extensive wrangling, electric lights were installed. In 1928, the church building was re-dedicated after the installation of the Rider Organ Company pipe organ, a gift from the Bemis Memorial Chuch (Universalist) in Lyndonville when it disbanded.

In the 1960's the church building and its furniture were again extensively renovated, with particular attention being dedicated to the exterior and the furnishings. A piano was donated to the church for use in services.

Dr. Venila Shores, in her "Lyndon: Gem in the Green" adds that the history of this church would not be complete without reference to its connection with the Lyndon Literary and Biblical Institute. Over the years between 1869 and 1882, the Baptist Church contributed mightily in time and money to the Institute, until the Institute failed financially. When the Institute re-opened two years later, one of the conditions was that the Institute be non-denominational, thus severing its connection with the Baptist Church.