The shooting happened Sunday around 3 a.m. at the restaurant on Highway 70.
Officials said the deputy was conducting off-duty security work at the time of the shooting.
According to a report from WCTI, Deputy Joseph Heck and Deputy William Shambeau were inside the Waffle House and walked outside to make a security check of the parking lot. The two officers saw William Gibbs III standing next to a car and firing a handgun at another person in the parking lot.
The officers demanded Gibbs drop the weapon, but he did not follow orders. Deputy Heck then shot Gibbs.
Gibbs later died at Lenoir Memorial Hospital.
The SBI is investigating the shooting.