Before the founding of Holy Trinity Church in 1918 (1918), Greek Orthodox Christians had to travel to Omaha, Nebraska to attend services. Paikos K. Pappaphilipopoulos, who would Americanize his name to "Peter Nelson", led the organization of a church. Their initial meeting was held at a Knights of Columbus Hall. In 1920, they purchased property near the downtown area for US$35,000 (equivalent to US$532,326 in 2023).[2] There was a house on the property that was used as the parish's first church. Father Constantinos Harvelas served as the church's first pastor.
The cornerstone for the present church building was laid in the spring of 1925 and the church was dedicated on 4 October 1925. It is the oldest and largest Orthodox Church building in Iowa.[2] In February 1996, a fire gutted the church's interior. Christ Kamages of San Francisco served as architect for the renovation while iconographer Elias Damianakis of Florida and woodcarver Steve Kavroulakis of Crete designed and built a new altar, sanctuary, narthex, iconostasion, and iconography. Metropolitan Iakovos of Krinis rededicated the church in June 1999.