In protest of this, the Daviess County Baptist Association in their annual 1895 meeting adopted a resolution stating that none in their churches could retain their membership if they were engaged in the retail or wholesale liquor business. This deeply divided the members of First Baptist Church and in a special meeting in July 1896, another resolution was adopted which stated the impossibility of the two halves working together peaceably. They would separate with an equitable division of property.
Pastor Dr. Fred. D. Hale and 491 temperance members of First Baptist left to form Third Baptist Church. The pro liquor members remained at First Baptist. On August 9, 1896, the congregation met in the Sam Jones Tabernacle on the northwest corner of Locust Street to witness the formal ceremony recognizing the new church. Some 2,000 people gathered, and over $18,000 was raised to build the new church here on Allen Street. By 1904, the congregation had swelled to over 1,000 members, the largest of any denomination in the area.
Reuben H. Hunt from Chattanooga, TN was the architect. He designed many churches, courthouses, and auditoriums throughout the South. Some of the notable features of the church are the large and beautiful stained glass windows and the acoustics. It has been the site of the Owensboro Chorale Society’s annual Christmas performance of the Messiah since it's first performance on December 7, 1941. This first performance was interrupted by the announcement of the bombing of Pearl Harbor. Comparison between Third Baptist Church and the Ryman auditorium, another Hunt creation, have been drawn regarding similar acoustics.
On October 18, 2007, a tornado touched down in the downtown area of Owensboro, including at Third Baptist Church. The church was evacuated minutes before the tornado hit, causing the steeple to collapse into the sanctuary. The damages cost about $7 million. The sanctuary was restored and officially reopened on Easter Day, April 12, 2009.