The burglars broke in by throwing a rock through a glass plate in the window, said Janea Boyles, a co-owner of the Mercantile.
"The burglars got in without tripping the alarm," Boyles told East Atlanta Patch. "They went directly for the cash registers."
The registers were empty but they managed to break one open in the burglary, which occured at 4:52 a.m.
It was the first such incident at the specialty foods eatery in its 4½ years of operation, Boyles said.
It took them less than a minute to be in and out. One of them had a gun, which could be seen in suveillance video taken of the break in, she said.
Though it's not clear enough to give a detailed description, one the of the burglars appears to a woman, Boyles said.
"We consider ourselves lucky," she said, noting the shop was closed at the time. "I am concerned because they were carrying a handgun."
Anyone with any information is urged to call 911.