During the mid 1960s, the Air Force was reorganized and the wing renamed Ala 16 as part of the newly formed Tactical Aviation Command.

Ala 12 acquired its current designation on 25 March 1971 and it soon began to receive the McDonnell Douglas F-4C Phantom II fighter aircraft.

In November 2003, Ala 12 flight hours on the Hornet exceeded 100,000, a total greater than that flown by any of the unit's previous aircraft types.

Ala 12's Hornets were the first Spanish aircraft to undergo a mid-life update, and in 2006, 122 Squadron was recognized by NATO an operational evaluation rating of "Mission Capable".

They provided the initial Spanish contingent of NATO forces in Operation Odyssey Dawn, the American-led portion of the 2011 military intervention in Libya, from 19–28 March 2011.