St. Paul's Lutheran Church in Union Township was organized on December 7, 1873. Their worship services were held in the Gardner school located a couple miles south of Grafton and they were served by a pastor from Nora Springs. In the late 1870s, a free Protestant group attempted to organize in Grafton, where a number of German Lutheran families lived. With the recommendation of Pastor Zeilinger of St. John's, St. Paul's was disbanded with some members going to St. John's and the remainder to a new congregation in Grafton. Unfortunately the St. Paul records have not been located.

Immanuel Lutheran Church was organized on January 1, 1883, when they adopted their constitution as a congregation of the Iowa Synod. Eventually Emmanuel came to be the established form of the church name. At that time, a church member was a voting member, which applied only to the male head of a household. His wife and any unmarried children were considered to be baptized souls and as communicants after they had been confirmed at about age fourteen years, but not members in the contemporary sense of the word. An 1897 membership list cites "110 members, 406 communicants, and 708 souls," or baptized members.

The first church, a frame structure, was built in 1888. In June 1935, construction of a new church was started. It was built with blended Kesota stone and trimmed with Indiana lime. It was dedicated on April 26, 1936.