Shortly after midnight, two individuals dressed in black with blue bandanas covering their faces entered the restaurant on Highway 491, Frank Fisher, a spokesman for the FBI, said in a news release.
Witnesses reported the robbers had an assault rifle.
The suspects took an undisclosed amount of money. They may have fled in a light-colored sedan.
Anyone with information is asked to call the Albuquerque FBI at 505-889-1300 or send a message to tips.fbi.gov.