On June 24 , 1571 , Spanish conquistador Miguel López de Legazpi arrived from New Spain ( now Mexico ) , and then exercised rule of the Spanish city of Manila as a territory of New Spain with the establishment of a city council in what today is the district of Intramuros . López de Legazpi had the local royalty executed or exiled , after the failure of the Tondo Conspiracy ; a plot wherein an alliance between Japanese merchants , Luzon 's Huangs with several Datus and Rajahs plus the Bruneian Empire would band together to execute the Spaniards and their Latin @-@ American mercenaries , and Visayan allies . At the conclusion of which , the victorious Spaniards made Manila the capital of the Spanish East Indies and of the Philippines , which the empire would control for the next three centuries , from 1565 to 1898 .