Investigators said two men walked into the restaurant at the 15000 block of Wallisville Rd. around 4:30 Tuesday morning, robbed the place and took off.
After a search, deputies detained two people. Officers were also searching a nearby school for suspects.
A man was placed in handcuffs at a shopping center near the Waffle House.
It's unclear how many people were involved.
The men who were questioned were released.