German immigrants settled in the nearby New Berlin community on Elm Creek in the 1870's and founded a congregation known as Christ Lutheran Church. After the arrival of the San Antonio and Gulf Railroad in 1893, many church members moved to LaVernia, and for a time, they made the weekly journey back to New Berlin for worship services. In 1901, however, 20 families gathered to form a local congregation to serve German Lutherans in La Vernia, and they called the Rev. H.W. Schmidt as their first pastor. Immanuel Lutheran Church members worshiped at the Presbyterian church until their own building was completed on this site on Cibolo Creek in October 1901. An associated cemetery (2.1 mi. NW) was established on donated land the following year. After Pastor Schmidt left in 1903, the church issued a joint call with Christ Lutheran Church for a new pastor, and this shared pastorate continued for many years. The congregation drew steadily under the leadership of the Rev. Nic Frueh, who served as pastor from 1911 until 1943. In 1932, due to deterioration and a violent storm, a new church building was erected to replace the original. During pastor Frueh's tenure, English-language services were added, and one member was ordained to the Lutheran ministry.

Although damaging floods in 1913, 1973, and 1998 have proved challenging for the congregation, the members have sustained their various ministries and programs, including education and outreach. Immanuel Lutheran church remains an important part of the ethnic and religious heritage of Wilson County.