In 1769, First Presbyterian was founded when its members decided to build their own wooden church structure.

Jonathan Trumbull Backus, for many years a trustee of Union College, pastored First Presbyterian from 1832 to 1872.

Under his leadership the congregation grew significantly and established East Avenue (now State Street) Presbyterian Church.

Backus was elected moderator of the Presbyterian Church in the United States of America in 1870.

Herbert S. Mekeel (minister from 1937 to 1979) was called to the church, and like Dr. Backus a century earlier, started it on the road to spiritual vitality once again.

Many members became dissatisfied and, in the first years of his pastorate, went over to the liberal First Reformed Church (RCA).

Mekeel held his ground, and the remaining congregation grew even larger and stronger than before.

The UPC adopted the Confession of 1967, which was effectively intended by its supporters to replace the Westminster Standards in the denomination and their high view of the authority of Holy Scripture.

In 1975, the congregation decided to petition the Presbytery of Albany to let First Presbyterian to change the denominational affiliation.

Albany Presbytery forcefully sought to bring the congregation to heel, including through an unsuccessful effort to lock officers and members of First Presbyterian out of the church's buildings.