Clayton police spokesman Tim Owens said the shooting happened about 5 a.m. today at a Krystal restaurant in Stockbridge.
Mr. Owens said the employee apparently got upset with the manager over a reduction in hours while the two were preparing to open the restaurant.
The employee's name was being withheld until relatives could be notified.
The manager was taken to a local hospital. Mr. Owens said her wounds were not life-threatening.