In July of 1898, 46 men met to take the first steps towards organizing a new congregation in Story City called Immanuel Lutheran Church. Because of certain doctrinal disputes, these men and their families had separated themselves from St. Petri Lutheran Church which had been established years earlier. During these early years Immanuel was linked as a parish to the South St. Petri congregation (now Gilbert Lutheran) and St. Paul's congregation (NW of Story City).
The need for a permanent church home resulted in the building of a frame church that was dedicated September 10, 1899. This church was just east of the present Story City Clinic parking lot. After some short-term pastoral help, the congregation voted in 1900, to extend a call to Pastor Thor T. Heimarck who served the congregation until his retirement in 1945.
After only 15 years the first church building was considered too small for the growing congregation. In October 1915, the vote was taken to build a new church with costs not to exceed $25,000. When the church was dedicated on July 1, 1917, the press reported, "The new Immanuel Church will undoubtedly take its rank as one of the fine pieces of architecture in Central Iowa."
In 1946 and again in 1951, congregational votes were taken as to whether St. Petri and Immanuel would again join together. The vote for unity was defeated but only by a narrow margin in 1951. During the early 50's a new organ was installed, women were granted the right to vote and plans were made for a new parsonage which was ready in 1954.