In early 1972 a small group of believers gathered to form what became Fellowship Baptist Church of Waterloo. They initially worshiped together in one of the small store fronts in the downtown area of Waterloo and later that year opened a new building at 1009 N Monroe Street. Between the years of 1972 and 1990 the small congregation experienced many difficult years, often with very few people in attendance.

In 1990 Fellowship Baptist Church called Todd Thelen as their new Senior Pastor. Shortly after, in 1992, the name of the church was changed to Prokopay Baptist Church. Through this time of blessing, God used Todd and Tammy Thelen to bring a fresh passion to Biblical preaching, refreshment to God’s people through shepherding, and a new vision for the community. The church continued to grow and by the mid-1990’s had around 100 in attendance. In 1999, Pastor Thelen and the leadership of the church proposed another name change, motivated by their ongoing pursuit for a biblical, independent and non-denominational future. Cornerstone Church was constituted in late 1999. After 10 years of faithful service, Pastor Thelen resigned and moved to another ministry in Nebraska in December 2000.