This article examines the repositioning of the Catholic Church in the aftermath of the Philippine Revolution of 1896–98, during the transfer of Spanish to American colonial rule. It reviews the consultations between the outgoing Spanish bishops and the Vatican’s Apostolic Delegate, Placido Chapelle, in January 1900, and the subsequent religious settlement promulgated in the Vatican’s Apostolic Constitution for the Philippine Church, Quae mari Sinico, in 1902. The Delegate’s identification with the Spanish bishops and their opposition to Filipino nationalist aspirations and the Filipino secular clergy confirmed the anti-Filipino position of the Church in the American colonial period. Both the Filipino bishops and the American bishops opposed independence and distrusted the nationalist leaders as anti-clerical Masons. This is followed by a discussion of the claimed reconciliation of Church and Filipino political aspirations in the post-Vatican II period in the 1960s, which culminated in the Church’s role in bringing down President Ferdinand Marcos in 1986. Committed to a theology of social justice, the bishops now aligned the Church with progressive democratic nationalists. In its successful opposition to the Marcos dictatorship in the name of “People’s Power,” the hierarchy claimed that through the “Miracle of EDSA” the Church had identified with and indeed represented the political will of the Filipino people.