In the heart of Jacksonville, Bethel Baptist Institutional Church is recognized as one of the historic monuments among churches in the State of Florida. In July 1838, Reverend James McDonald assisted by Reverend Ryan Frier, organized the first Baptist church in Jacksonville under the title Bethel Baptist Church. There were six charter members: Reverend James McDonald, the first pastor, and his wife; Mr. Elias C. Jaudan, who became the first deacon, and his wife; and two slaves known as Bacchus and Peggy. The first racially mixed meetings were held in the Government Block House, which stood near the County Courthouse. In 1840, the church purchased a lot on the northeast corner of Duval and Newnan Streets and built their first house of worship. The Legislative Council of the Territory of Florida incorporated the Bethel Church on February 10, 1841. William B. Kass, Charles Merrick, Soloman Warren, Elias Jaudan, H. H. Phillips, and A. Ossian Hart, the first trustees, were a part of the incorporation. The church later moved to the LaVilla Area between Duval and Adams Street.

Deacon Jaudan purchased a lot on Church Street, between Hogan and Julia Streets, and gave it to the church. A new church was built and the congregation entered the new building in the spring of 1861. Soon after the congregation started worship services in the new building, the Federal Army took possession of the Bethel Church and used it as a military hospital for wounded soldiers during the Civil War. The church was left in deplorable condition when vacated by the army troops. At the close of the Civil War, an effort was made to separate the Colored and White members but an agreement could not be reached over possession of the property. The opposing fractions went to court and the decision was in favor of the Colored members since they were the majority. They retained the name of the Bethel Baptist Church and were the rightful owners of the Church Street property. A short while after the court’s decision, the Colored members sold the property on Church Street to their White brethren and purchased a lot on the northwest corner of Union and Pine Streets (now Main). In 1868, they erected a one-room frame building where the Bethel Baptist Church congregation worshipped for twenty-seven years and grew from a few souls to several hundred. Also from the separation, the White members established the Tabernacle Baptist Church, located on Church Street, which was later named First Baptist Church (Downtown).

The congregation grew rapidly, over the years, so much so that more space was needed for worship and for training. The building could not be repaired or enlarged because of the extended fire code of the city of Jacksonville. Reverend J. Milton Waldron, Bethel’s fifth pastor, led the congregation in replacing the one-room frame building with a larger more attractive brick house of worship. In 1895, Bethel constructed the first Institutional Church building ever erected in the South by a Colored congregation. It was built of red pressed brick, trimmed with Georgia Marble. The building contained a main auditorium with a seating capacity of 1150 and nine classrooms at a cost of $26,000. It was erected by Colored mechanics under the direction of Colored contractors. This beautiful edifice was in use only a short time before the devastating fire of Jacksonville destroyed it on May 3, 1901. After the fire, the membership bought the River Square bound by Hogan (now McKissick Street), Eagle (now First Street), Julia and Caroline (now Bethel Baptist Street) and began preparations for rebuilding. During this period, the Church established temporary quarters for church services and the Bible Institute in a building that they labeled the “Shack”. Regular services continued in the “Shack” until the completion of the Historic Sanctuary in 1904. The new edifice was not only a church of worship, but it also served as a training center to help Christians prepare for service to mankind.