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.
Perdido Bay Baptist called their pastor, Chris Linsky, on May 1, 2022.