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On December 10, 1799 public notice was given for a meeting to be held on January 2, 1800 to elect trustees for a "Presbyterian Church to be established in the village of Lyons in the town of Sodus." Services were first held in a farm and later in a storehouse which was moved to a lot "set aside for gospel purposes." On October 23, 1809 Rev. John Lindsley, a missionary of the General Assembly organized the church further, and the session began meeting. Until 1820 the original name of the First Presbyterian Church in Sodus was retained. At that time the legislature was petitioned to change the name to the First Presbyterian Church and Society of Lyons.

In 1825 the church had outgrown its quarters and a new brick church was completed. Between 1826 and 1834 a series of revivals added 224 new members. A Sunday school was established in 1814 and in 1825 the Female Missionary Society of Lyons began. In 1805 Charles Williamson had given the church 150 acres, the income of which was used to pay the pastor. An act of the state legislature was required to allow the church to sell the lot in 1866. In March, 1849 construction was begun on a new building which was dedicated the following February. In 1851 there was another revival season and again in 1870 and in 1880-1881.

Between 1866 and 1872 a strong effort was made to have the owners of the pews release their titles to the church in order to increase church income. See the anniversary booklets in the accessions folder for additional historical information, a list of pastors and biographies of prominent members.