A powerful new Jet Age began at Moffett Field with the start of the Korean War in 1950. Carrier-based fighter and attack squadrons were moved to the base, and fighter jet pilots were trained onsite. In 1950, Moffett Field was recognized as the first of nine all-weather naval air stations.

In 1951, in order to serve faster aircraft capable of flying at higher altitudes, new support buildings were added, both runways were resurfaced and extended, taxiways were expanded, new parking and apron areas were constructed, and an innovative, high-speed refueling system was added. Three new high-explosive magazines and an ordnance handling pad were also built. A fuel transport and storage system, consisting of a barge canal, dock, wharf, pipeline, and fuel farm east of Hangar 3, was completed in 1953.

Commissioned at Moffett Field in 1951, Fleet Aircraft Service Squadron (FASRON) 10 was one of the first all-jet FASRON groups in the Navy. Hangars 2 and 3 were used to provide maintenance services and repair aircraft that were damaged while serving in the Pacific Fleet. In 1953, Moffett Field was designated one of the Navy's nine "Navy Master Jet Stations.'' F3D Skynight, F2H Banshees, F3H Demons, FJ-3 and FJ-4 Furies, F7U Cutlasses, AD Skyraiders, F9F Panthers and Cougars, F4D Skyray, and subsonic A4D Skyhawks all took flight from Moffett Field. Nearly every new supersonic jet fighter aircraft used by the U.S. Navy and Air Force in the early 1950s was flight-tested at Moffett Field, including F8U Crusaders and F11F Tigers. Jet aircraft squadrons were based at Moffett Field until 1961, when Naval Air Station Lemoore in California's San Joaquin Valley took over operations that were deemed too loud to continue zooming above the densely populated Bay Area and potentially risky as the air traffic from the region’s three civilian airports increased.

The next phase of the HTA era at Moffett Field began in 1962, when it was chosen as the West Coast training center for the Navy’s anti-submarine operations. Just like the rigid airships and blimps that patrolled the Pacific, the new propeller-driven Lockheed P-3 Orion aircraft was designed to fly long missions at low-altitudes and slow speeds to hunt for threats above and below the ocean’s surface.

The four-engine turboprop P-3 could reach a maximum speed of 405 miles per hour and had a range of 5,570 miles. Its crew of up to 12 people, including three pilots, could extend their 10 or 12-hour missions by shutting down one of the P-3’s four engines to conserve fuel. Throughout the Cold War, Soviet submarine activity was tracked using a Magnetic Anomaly Detection boom at the end of the fuselage and sonobuoys that were dropped from the plane into the waters below and then monitored by radio. The aircraft also had an internal bomb bay that could house torpedoes, nuclear weapons, mines, missiles, and bombs.

Moffett Field was the command center, administration, and training facility for all Pacific anti-submarine operations and became the largest P-3 base in the world. Pilots and technical crews received their training in an area of the airfield nicknamed “Orion University.” That zone included Hangars 2 and 3, which could each hold up to 12 aircraft.

A total of nine P-3 patrol squadrons were stationed at Moffett Field during the period of 1963 until 1993: VP-31 "Black Lightnings/Genies," VP-9 "Golden Eagles," VP-19 "Big Red," VP-40 "Fighting Marlins," VP-46 "Grey Knights," VP-47 "The Golden Swordsmen," VP-48 "The Boomerangers," VP-50 "Blue Dragons," and VP-91 "Black Cats" reserve squadron. In 1973, Moffett Field became the headquarters of the Commander of the Patrol Wing for the U.S. Pacific Fleet, which was responsible for patrolling 93 million square miles of ocean from Alaska to Hawaii.

In 1990, Congress passed the Base Closure Act, which aimed to save money by identifying and shutting down military facilities that were deemed unnecessary after the fall of the Berlin Wall and the collapse of the Soviet Union. The Federal Base Realignment and Closure Commission (BRAC) placed Naval Air Station Moffett Field on the list of recommended base closures in 1991. Over the next three years, Moffett Field’s P-3 squadrons were either retired or relocated to Naval Air Station, Whidbey Island, Washington and Naval Air Station Jacksonville, Florida. The last active duty P-3 squadron departed on December 21, 1993. The reserve squadron VP-91 continued its operations at Moffett Field until 1999. On July 1, 1994, Naval Air Station Moffett Field was decommissioned. NASA became the steward of the majority of the site, and Hangar 3 became the home of the 129th Rescue Wing of the California Air National Guard.