Flight operations were launched on 25 May of that year, initially on regional chartered routes on behalf of Occidental Petroleum, a US-based oil and gas company.

When Faucett and Aéroperu both went bankrupt in 1999 due to financial difficulties, Aero Continente acquired a monopoly position as the only airline operating on domestic routes in the country.

In 2002, the company suffered a setback when Chilean authorities arrested several staff members of Aero Continente Chile over drug trafficking allegations, which forced the airline to cease all flight operations.

In 2003, after the Dominican subsidiary had failed, Aero Continente itself opened a small base Santo Domingo Airport, offering VFR flights to the Hispanic population centers in New York City, Los Angeles and Madrid.

Thus, Aero Continente lost its insurance protection, as Global Aerospace, a partly US-based company that was responsible for this matter, was forced to cease its involvement with the airline.