On March 24, 1999, with the intensification of conflicts in the Kosovo region of the former Federal Republic of Yugoslavia, NATO initiated Operation Allied Force, with Portuguese F-16s actively participating in NATO operations to contain the humanitarian crisis in the Kosovo region.
The national participation in Operation Allied Force highlighted and demonstrated the maturity of the capability, as well as the versatility of national aircraft and crews, effectively consolidating the country's commitment to international peace and security.
During this period, the national F-16s operated from Aviano Air Base in Italy, often conducting missions exceeding 7 hours of flight time, utilizing multiple in-flight refuelings.

The national deployment consisted of 3 F-16A aircraft and 60 military personnel (pilots, mechanics, and operations support staff). The national participation was marked by a total of 281 sorties with 1050 flight hours.
The national aircraft carried out Combat Air Patrol (CAP) and aerial surveillance missions over Albania, the Adriatic, Hungary, and the territory of the former Yugoslavia, ensuring the integrity of the no-fly zones against opposing forces.