It happened around 7:40 p.m. Friday on the 2100 block of Orthodox Street.
Police said the owner had a gun and fired at two robbers who came into the store.
A 32-year-old employee was shot in the arm.
Police are not sure at this time if the victim was accidentally shot by the owner.
He was taken to the hospital in stable condition.
The search continues for the two suspects who fled the scene.