The base was established on 21 October 1964, originally built to serve as a training facility for the German Air Force (Luftwaffe), due to airspace limitations within West Germany.

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

[2] Between 1993 and 2018, the PoAF has operated Dassault/Dornier Alpha Jet aircraft from the airbase, which were donated by Germany as compensation for leaving the air base in 1993.

[2] Beja Air Base is one of the most important training facilities of the PoAF and during 2008 operated over 70,000 flying hours.

The Portuguese wet lease airline Hi Fly previously operated its A380, purchased second-hand in 2018, from Beja.