German settlers in Waterhouse began worshiping together in 1893. Officially named St. John Lutheran Church in 1895, the congregation moved to Glen Flora in 1920 after storms destroyed its first three houses of worship. The Glen Flora sanctuary, built in 1920, was destroyed by a 1929 tornado. In 1941 the congregation moved to Wharton, taking with them the small frame sanctuary they had built in 1929. Renamed St. Paul Lutheran Church, the congregation eventually erected larger facilities at this site.