Until 1993, it was used particularly for weapons training, and in 1987 the Portuguese Air Force's 103 Squadron and its Lockheed T-33 and Northrop T-38 aircraft was relocated from Montijo.

[2] After their arrival, the base started to host a mixed array of fixed and rotary-wing trainers, as well as maritime patrol aircraft.

Along with the airports in Lisbon, Porto, Faro, Funchal (Madeira), Porto Santo, Flores, Santa Maria, Ponta Delgada and Horta, the airport's concessions to provide support to civil aviation was conceded to ANA Aeroportos de Portugal on 18 December 1998, under provisions of decree 404/98.

[3] In 2011, a new civilian terminal was built and Beja became a dual-use military-civilian airport, aiming to attract low-cost carriers.

It may possibly be a logistics platform between the goods that are shipped to the nearby Port of Sines and the whole of Europe.