The mission of the Air Defense Command is "to defend, secure and protect the territory of the Republic of the Philippines." Its is tasked to oversee the Philippine Air Defense System and further provide the tactical air operation requirements within its area of responsibility. Under its operational control are the 5th Fighter Wing, 580th Aircraft Control & Warning Wing and the Composite Tactical Group (1, 2 & 4).

The mission of the Tactical Operations Command is "to conduct tactical air operations in support to the Armed Forces of the Philippines (AFP) forces." It is tasked to provide close air support to AFP ground forces; conduct aerial reconnaissance, medical evacuation, disaster relief & rehabilitation, combat search & rescue; and performs aerial activities to support the government in nation-building and socio-economic activities. Further it develops, operates and maintains strategically located air bases and stations. Under its operational control are the 560th Composite Tactical Wing, 530th Composite Tactical Wing and the Composite Tactical Group (6, 9, 10, 11 & 12).

The Air Logistics and Support Command provides logistics, maintenance and engineering support to the Philippine Air Force. Under its operational control are the 355th Aviation Engineering Wing, 410th Maintenance Wing, 420th Supply Wing and the Air Force Research & Development Center.

The Air Reserve Command, a support command, manages the inactive reservists of the Philippine Air Force through various Reserve Air Transport Support Groups (RATSGs) and Air Reserve Wings.