Manila was founded in 1571 by Spanish conquistadors. In 1867, the Spanish Government of the Philippines founded the municipalities and territories south of the District of Morong in Nueva Ecija, north of the Province of Tondo and Imperial Manila, and isolated these from their mother province-Nueva Ecija. The Government created the Province of Manila composed of the Province of Tondo to the south and the isolated territories of Nueva Ecija to the north. The parts of Tondo were Navotas, Malabon, and Caloocan; and the parts of Nueva Ecija were Mariquina, Balintawak, Caloocan, Pasig, San Felipe Neri (presently called Makati), Las Piñas, what had been known as Paranaque, and Muntinlupa were combined to form the Province of Manila. The capital of the Province was Intramuros, then itself called and considered to be Manila, a walled city located along the banks of Pasig River and Manila Bay in the present Manila.

In 1897, while the Imperial City of Manila is being prepared for industrialization, most houses in Tondo were demolished to give way to railroad construction. One of those whose house was demolished was Andres Bonifacio, the founder of the Kataastaasan, Kagalanggalangan, Katipunan ng mga Anak ng Bayan (Supreme and Revered Union of the Children of the Nation) or KKK, a secret organization which aimed towards independence and self-governance away from the Spanish government. In 1896, the Cry of Balintawak was initiated, an event which denounces the Spanish authority by tearing their cedulas or residence tax slips. On December 30, 1896, Jose Rizal, the Philippine National Hero, was executed by the Spanish government in Bagumbayan, an execution site near Intramuros. This event led to the Filipino uprising against Spain. Likewise, The Province of Manila was the 8th and last Province to revolt against Spain paving the establishment of the Federated Philippine Republics (composed of Nueva Ecija, Pampanga, Bulacan, Tarlac, Laguna, Batangas, Cavite and Manila). The Province remained in existence until 1901, when its territory was subdivided by the Americans.

In 1901, the Philippine Assembly created the City of Manila composed of the Municipalities of Ermita, Intramuros or Imperial City of Manila, Tondo, Santa Cruz, Sta. Ana, San Nicolas, San Miguel, Paco, Port Area, Pandacan, Sampaloc, Quiapo, Binondo, Malate, Sta. Mesa and Singalong. Some Assemblymen included the municipalities of Caloocan, Marikina, Pasig, Parañaque, Malabon, Navotas, San Juan, Makati, Mandaluyong (San Felipe Neri), Las Piñas, Muntinglupa and Taguig-Pateros to a new province named Rizal. The capital of the province was Pasig.

In 1941 as an emergency measure, President Manuel L. Quezon created the City of Greater Manila, merging the city and municipal governments of Manila, Quezon City, San Juan del Monte, Caloocan, etc. and appointing Jorge Vargas as Mayor. Existing mayors of the included cities and municipalities served as vice-mayors for their areas. This was in order to ensure Vargas, who was Quezon's principal lieutenant for administrative matters, would have a position of authority that would be recognized under international military law. There were doubts if the Japanese Imperial Army poised to occupy Manila would recognize the authorities of members of the Quezon cabinet. The City of Greater Manila was abolished by the Japanese with the formation of the Philippine Executive Commission to govern the occupied regions of the country. As an administrative concept, however, the City of Greater Manila served as a model for Metro Manila and the position of Metro Manila governor established during the Marcos administration.

In 1975, owing a great respect to the history of Manila, President Ferdinand Marcos issued Presidential Decree 824, creating the Metropolitan Manila Area. The site of the old province of Manila can no longer be used for agricultural purposes and therefore the term 'province' is not applicable. The decree seceded the 12 municipalities and 3 cities of Rizal, the municipality of Valenzuela in Bulacan and Manila. The Metropolitan Manila Commission is created to administer the emerging metropolis. Marcos appointed his wife Imelda Marcos as governor of Metro Manila.

In 1986, after a major government reorganization, President Corazon Aquino issued Executive Order No. 392 and changed the structure of the Metropolitan Manila Commission and renamed it to Metropolitan Manila Authority. Metro Manila Mayors chose from themselves as chair of the agency.

In 1995, through Republic Act 7924, Metro Manila Authority was reorganized and became the Metropolitan Manila Development Authority. The chair of the agency is appointed by the President and should not have a concurrent elected position such as mayor.