The franchise began in 1959 as the Charleston White Sox of the South Atlantic League (now the Southern League); it subsequently moved several times, playing in Charleston, South Carolina, (1959–1961); Savannah, Georgia, (1962); Lynchburg, Virginia, (1963–1965); and Evansville, Indiana, (1966–1968), before moving to Columbus, Georgia, in 1969 to play in Golden Park.

Additionally, as Pensacola is within the franchise territory of the Mobile Bay Bears, Studer paid that team an undisclosed sum of money.

[4][5] The Blue Wahoos nickname was decided in a fan contest run by Wendy's in conjunction with the Pensacola News Journal.

[8] In 2016, the Blue Wahoos were chosen by Baseball America as the Double-A winner of the prestigious Bob Freitas Award as the best overall franchise among the nation's 30 affiliates at this level.

It was announced at the Baseball Winter Meetings at the Gaylord Resort and Convention Center in National Harbor, Maryland, just outside of Washington, D.C.

The Blue Wahoos are also televised on delay Monday through Thursday on Cox Sports and Friday through Sunday on Blab-TV (WFBD).