With the outbreak of the Korean War, the United States Air Force took interest in the former Naval Station for use as a Basic Military Training (BMT) Base. Custody of the most of the property of the training center was transferred to the Air Force in 1950, and the Air Force named the facility Sampson Air Force Base on 15 November 1950. With the Air Force establishing Sampson AFB, the park project was cancelled.

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The Air Force spent about $6 million on renovations and beginning in February 1951 started training what would be 16,000 Air Force recruits. Air Training Command (ATC) established the 3650th Indoctrination (later Military Training) Wing to manage the base and conduct Basic Training, as its major facility at Lackland AFB, Texas was overflowing. During the first two weeks of 1951, the population at Lackland AFB jumped from 36,513 to over 70,000 people. In addition, a third BMT center was established at Parks AFB, California to accommodate new enlistees. The mission of Sampson AFB was to provide formal basic training for all male and female enlisted personnel not having sufficient previous military training; to establish and operate such assembly, processing and separation station as specifically directed; to provide a comprehensive counseling program for Basic Indoctrinee personnel in order that these airmen may be most effectively assigned in accordance with Air Force requirements; and to maintain training programs for accomplishing rehabilitation of garrison prisoners. The first trainees arrived on 1 Feb 1951. The base employed about 700 civilians and had 600 permanent party troops.

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During the years before the Korean War, basic military training had lasted anywhere from 4 to 13 weeks. In the rush to flow recruits through the training system and into the theater of conflict, ATC reduced the course to seven weeks in 1950 and then to two weeks in January 1951. With the opening of Sampson and Parks AFB for BMT, Shortly thereafter, ATC increased basic military training from seven weeks to eight. In July 1952 the Air Staff approved a 12-week course, which ATC implemented on 1 August at Lackland and Parks and on 1 September at Sampson. However, after only two months, the Air Staff decided that the course should be shortened, and ATC developed an 11-week program to begin in January 1953. The host organization at Sampson was redesigned as the 3650th Military Training Wing, Air Training Command, in March 1953.

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The Air Force also built a runway and other facilities at Sampson and converted the base to its needs. By 1953, a single paved 5,000 foot north–south runway (Rwwy 17/35) was completed and a control tower, fire station and aircraft parking ramp was built on the west side, with B-25 Mitchell, C-47 Skytrain, and C-45 Expeditor aircraft assigned.

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With the end of the Korean War and cutbacks in the military budget afterwards, Air Training Command discontinued its basic training school at Sampson AFB on 1 July 1956. Shortly thereafter, ATC discontinued Sampson's 3650th Military Training Wing. By the time it was closed, over 300,000 airmen received basic training at Sampson AFB in preparation for service in the Korean War, as well as service in USAFE, Far East Air Force, and other United States Air Force major commands both in the United States and around the world.

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Three months later, on 1 October 1956, control of Sampson AFB was transferred to the Rome Air Force Depot, Air Materiel Command and the base was placed in standby status.