The Kentucky State Police said the white male suspect was inside the church and was shot by a Shelby County deputy after ignoring repeated requests to drop a weapon. Police have not identified the type of weapon.
The name of the suspect is being withheld pending notification of the family.
Simpsonville Baptist reported an earlier break-in Thursday morning.
Church members spent several hours cleaning staff offices and the fellowship hall of scattered debris and spray painted graffiti.
Authorities said because of the first burglary, security personnel were posted overnight at the church. It was the church’s private security who contacted police of the second break-in around 2:46 a.m. Friday.
It isn’t clear whether the same suspect was responsible for both break-ins.
Kentucky State Police said the investigation is ongoing.