In the context of the Second World War, in July 1941, a Portuguese mission under the command of engineer Colonel Hermínio José de Sousa Serrano, and which included Colonel Frederico Lopes da Silva and Major Fernando Tártaro, visited Santa Maria to study a possible location for an airfield, opting for the plateau known as Pico de Maria Dias. Two years later, technicians from Pan American World Airways arrived on the island, arriving on board the NT Lima in December 1943, and confirmed that the location was optimal for establishing a military airfield to complement the field at Lajes. The airfield would, therefore, assist in the protection of the maritime convoys that crossed the Atlantic to support the port of Murmansk in the Soviet Union, which were being sunk by German U-boats.

The project that was planned, and which was sent for approval to António de Oliveira Salazar, included provisions for an inter-island and a trans-oceanic airport, with the first costing 1.685 million US dollars, and the second 5.125 million US dollars. The final plan, sent to the Portuguese government by Pan American, and contracting the construction was an estimated 3.130 million US dollars, and included:

Construction of two piers at the port;

Expansion of the wharf and ramp;

Improvements to the roads, bends and bridges;

Construction of a roadway to the aerodrome;

Construction of three runways: 2 2,000 by 50 metres (6,560 ft × 160 ft) and 1 1,400 by 50 metres (4,590 ft × 160 ft), with an area of 270,000 square metres (2,900,000 ft2);

A platform/tarmac for parking aircraft that was 150 by 150 metres (490 ft × 490 ft);

A control tower and station building; and

A water supply and sewage network.

Military airfield

While the final project was being prepared, the Portuguese Department of Defense authorized immediate execution of the first work, that included a runway to service planes transferred from Lajes Airfield, carrying with them the technicians and equipment. Along with a team of little more than 40 workers, Lieutenant Engineer Correia de Sousa concluded the runway construction. On 8 August 1944, at about 2:15 p.m., the first plane landed on the runway, a Douglas C-47 Skytrain (Dakota C-47) operated by the US Air Force, transporting materials and bread from Terceira. It departed an hour later.

The Americans later extended the taxiways by another 200 metres (660 ft), and on 15 November 1944 a new 1,350 by 50 metres (4,430 ft × 160 ft) service runway was concluded (and which operated until 14 May 1945. The first runway was situated in the locality of Ginjal, it was a dirt runway covered with reinforced steel gridwork.

Finally, on 28 November 1944, an accord was signed between the US and Portuguese governments, that envisioned its use as a waypoint for planes travelling to the Pacific theatre of operations, or those that needed to be diverted due to weather conditions. This was followed on 14 December 1944 by a similar accord between Pan American Airways and the Portuguese government, resulting in the installation of new radio equipment. Work on the passenger terminal and support buildings had already progressed, along with runways 2 and 3 and the parking area. At this time there were 3000 workers onsite: 2000 American, 600 Micaleanse and 400 Marienses, a number that continued to grow over time (eventually reaching 3000 Americans and 1000 Azoreans). Meanwhile, the port was expanded to receive battalions with the equipment necessary to improve the infrastructures and to construct a network to pipe aviation fuel to the plateau. These included: airport infrastructures; roadways; water supply and sewage; residences; and social spaces (such as hotel, gymnasium, church, a cinema/theatre to hold 1000 people, and a hospital in the area of Santana, to evacuate the injured in the European theatre).

On 11 July 1945, the first Portuguese-registered aircraft landed in Santa Maria, an Avro Anson Mk I from Terceira's Air Base No.4 (Lajes Airfield), followed by a C-54 "Skymaster" on 24 July from São Miguel, that included various Portuguese and American authorities visiting the installations to officially inaugurate the aerodrome on 26 July 1945. The aerodrome was operated by American forces until the end of the conflict, and accounted for 500 airplanes that transited the site.

Civil aviation

The accords between the Portuguese, Great Britain and the United States permitted those forces to use the facilities in Lajes and Santa Maria until 2 June 1946. At that time the American forces base was transferred to Lajes and both airports began to be administered from Portugal. By Decree-law 35/736 (5 July 1946 the airport at Santa Maria began to be administered by the Secretariado da Aeronáutica Civil (Civil Aeronautics Secretariate), later substituted by the Direcção Geral de Aeronáutica Civil (Directorate-General for Civil Aeronautics). After improvements to the runway, the airplane parking area and installations in the terminal, the airport was inspected by Lieutenant-Colonel Humberto Delgado (then-Director-General of the DGEC), for it to be certified for operational traffic.