Het vliegveld wordt bestuurd door de Manila International Airport Authority (MIAA), een onderdeel van het Filipijnse Ministerie van Transport and Communicatie (DOTC).
Philippine Airlines (Bangkok, Busan, Fukuoka, Guam, Ho Chi Minhstad, Hongkong, Honolulu, Jakarta, Las Vegas, Los Angeles, Melbourne, Nagoya-Centrair, Okinawa, Osaka-Kansai, San Francisco, Seoel-Incheon, Singapore, Shanghai-Pudong, Sydney, Taipei-Taiwan Taoyuan, Tokio-Narita, Vancouver, Xiamen)
South Wing
Philippine Airlines (Bacolod, Butuan, Cagayan de Oro, Cebu, Cotobato City, Davao, Dipolog, General Santos, Iloilo, Kalibo, Laoag, Legazpi, Puerto Princesa, Roxas City, Tacloban, Tagbilaran, Zamboanga)
Air Philippines (Bacolod, Cagayan de Oro, Cebu, Davao, Dumaguete, General Santos, Iloilo, Naga, Puerto Princesa, Tugueragao, Zamboanga)
Manila Domestic Passenger Terminal
Asian Spirit (Angeles City, Baguio, Basco, Busuanga, Calbayog, Catarman, Caticlan, Davao, Masbate, Pagadian (seasonal), San Fernando, San Jose (Antique), Surigao, Virac)
Cebu Pacific (Bacolod, Butuan, Cagayan de Oro, Cebu, Cotabato City, Davao, Dipolog, Dumaguete, General Santos, Iloilo, Kalibo, Laoag, Legazpi, Puerto Princesa, Roxas City, Tacloban, Tagbilaran, Zamboanga City)