Perdido Bay Baptist was planted by Myrtle Grove Baptist Church in 1987.

The church held its first worship service on February 15, 1987 at the Perdido Chapel Funeral Home. July 19th of the same year the church moved into their permanent facility at 12600 Sorrento Road in Pensacola. Since then the people of Perdido Bay Baptist has served the Perdido, NAS Pensacola, and southwest Pensacola communities.

Currently, the church serves the community through its Food Bank every Wednesday morning. Further, Perdido Bay has partnered with other community churches and participates in the monthly Bay Area Food Bank.

Perdido Bay Baptist called their pastor, Lonny Hughes, on May 1, 2013.