The Rev. John Nelson organized a congregation of the Free Will Baptist Church (Free Mission Baptist Church) in the coastal town of Indianola in 1872. Three years later, a devastating hurricane struck the Texas Gulf Coast, inflicting major damage on Indianola. The Rev. Mr. Nelson and his congregation repaired their church, but in 1886 another hurricane completely destroyed the town. Many Indianola residents moved to Port Lavaca to begin new lives.
In 1898 the Free Mission Baptist Church members purchased a warehouse at this site and converted it for use as a house of worship. The name of the church was changed about 1900 to Saint Joseph Baptist Church, and following Nelson's death the congregation was served by traveling ministers. The church established a cooperative relationship with Mount Sinai Baptist Church, and the two institutions often shared services.
The original warehouse/church structure was replaced by a new building in 1984. Counting among its members descendants of its founders, Saint Joseph Baptist Church continues to serve the community with a variety of worship, educational, and outreach programs. (1992)