Holy Trinity Lutheran Church was begun in 1947 when a small group of men and women sought the help of Rev. Conrad Buehler of St. John in Montgomery to help determine whether another Protestant church could be established in New Prague. After study of the community, a new congregation was allowed to begin under the direction of the American Mission Board.

On June 15, 1947, the first service was held at the Z.C.B.J. Hall in New Prague. About 100 people attended. The mission was organized into a full-fledged congregation on May 23, 1948, and the first pastor was called. However, after a short stay, the pastor resigned and the Mission board withdrew its support. The congregation then sought help to continue its course through Gustavus Adolphus College in St. Peter, MN. They agreed to assist as much as possible, and the Rev. Arnold Carlson, Prof. of Christianity served as supply pastor from January until September. At an organizational meeting on April 3, 1949, the congregation was incorporated as a congregation of the Augustana Synod. The petition was granted, and in the spring of 1949, Holy Trinity purchased land on the corner of Third Street and First Avenue NE in New Prague. The cost of the land was $1700. A church and parsonage were built on that site. An additional education unit was added later. By 1977, the congregation had outgrown its quarters. It was decided to move to the current location on the east side of New Prague on Highway 19 (Doherty property). Ground was broken in April 1978. Construction was completed in the fall, and the first service in the new building was on December 17, 1978.

Ground was broken on an Education and Fellowship addition on October 15, 1989, and the building was completed in April of 1990. In 1992, a new Roger’s Organ and Pipes, a new sound system and Carillon Bells were dedicated. In 1996, the parking lot was expanded and in the fall of 1997 the congregation added a second Education hour and Relational Confirmation was introduced. Sonshine Christian Preschool was born in the summer of 1998 with 39 students. In 1998, a new Video Projection System was purchased. At full capacity, Sonshine gained license for a second class in 2002 and again expanded in 2005 for up to a total of 160 students.