The cornerstone for the second ediface of First Congregational Church was laid on September 22nd, 1868. On October 14th, 1869, the second church, which "cost about $140,000 ... was dedicated by the pastor and the presentation made by the Honorable Bradford R. Wood" one of the founders of the church and the President of the Board of Trustees. The dedicatory prayer was delivered by Dr. Palmer. The church was described in the leading newspapers as the "finest specimen of Romanesque style of architecture in this city." 

In 1900, an inspiring semi-centennial celebration was held in the church to mark its fifty years of continuous service in Albany. Famous men and women had spoken from its pulpit, it had taken a leading part in every forward movement, impressive Forefather’s Day services had been conducted, stimulating overflow meetings held in its lecture rooms, and concerts, plays and pageants presented in the large Sunday School Rooms.

At this celebration, special services honored Dr. Ray Palmer. A tablet in his memory placed on the outside wall of the church on the Jay Street entrance, was unveiled by his daughter, and his son, The Rev. C. R. Palmer gave the dedicatory address. The celebration also featured short addresses by Dr. Smart, Rev. Thrall, Rev. Marvin, A.S. Kibbee, Professor Oscar D. Robinson, Dr. George Gorham, David A. Thompson, and Harlan P. French. Also noteworthy: "The Sunday School Orchestra furnished music for the affair."

Shortly after the turn of the century, the diary of one member indicates individual communion cups were used for the first time in 1903."  The use of individual communion cups is a practice that remains in effect to this day at First Congregational Church.

 A short time later, the “Ray Palmer Club,” was established in 1905 by David A. Thompson, and included Congregationalists from Albany, Troy, Schenectady, Rensselaer and Saratoga churches “to encourage friendly relations among Congregational members.”

 In 1905, the Rev. Chares Hagar was called to be minister of First Congregational Church.