On March 27, 1843 a portion of the congregation of the Methodist Episcopal Church of Seneca Falls seceeded and organized the First Wesleyan Society of Seneca Falls at the school house. They built a church costing $1770 on a lot costing $600 at the corner of Hynderse and Fall Streets. That same year, many congregationalists who had joined the Presbyterian Church after their church had disbanded, withdrew over the question of American slavery and joined the Wesleyan church. In 1852 an effort was made to revive the Congregational church, and Rev. B.F. Bradford, who had served the Wesleyan church for 3 years was called to the pastorate. For a year and a half the group worshipped in the concert Hall, but Mr. Bradford's health was impaired, and the group disbanded. Most of the group returned to the Wesleyan congregation where they remained until 1869 when Rev. Lyle, the minister,
left the Wesleyans after being foiled in an attempt to transform that church into a Congregational church. Mr. and Mrs. Jabez Matthews and Abram Failing were prominent members who went back and forth between the two groups. The Congregational group called themselves the First Congregational Church of Seneca Falls, and met in the Good Templar's Hall in December 1869 with 63 members.
The split left the Wesleyans with only 60 members down from a high of 200 in 1862, but by 1875 the church was strong enough to dedicate a new church, valued at $14,500. The Sunday School was active, and the church possessed a library of 550 volumes.