Many of the airline's flights were operated on a regular basis, such as the ones from Belgium and New York to the Luis Munoz Marin International Airport in San Juan, Puerto Rico. But most of their flights, such as the ones from San Juan to Miami International Airport were operated on a charter basis. Usually, the SJU-MIA flight was operated for tour companies that then rented buses to transport their customers to Disney World in Orlando.
Capitol Air also operated many charter flights for the United States military. The airline used McDonnell DouglasDC-8 and DC-10 equipment.