In the first days of Baldwin County, the town of McIntosh Bluff (now in Mobile County, west of Baldwin County) on the Tombigbee River was the county seat. After being transferred to the town of Blakeley in 1810, the county seat was later moved to the city of Daphne in 1868. In 1900, by an act of the legislature of Alabama, the county seat was authorized for relocation to the city of Bay Minette; however, the city of Daphne resisted relocation. The citizens of Bay Minette moved the county records from Daphne in the middle of the night on October 11–12, 1901 and delivered them to the city of Bay Minette, where the Baldwin County seat remains to this day. Bay Minette was not incorporated as a city until 1907. A mural for the new post office built in 1937 was commissioned by the WPA and painted by Hilton Leech to commemorate this event.
In September 2011, the town attempted to enact a program called "Operation Restore Our Community". It would have allowed those convicted of a misdemeanor to substitute imprisonment with mandatory church attendance for one year. However, this program was challenged due to violating separation of church and state, and the program's start was delayed for judicial review. It appears to have been scrapped.