A large American military force was needed to conquer the country, and would be regularly engaged in war against Filipino forces for another decade. Also, Macabebe Filipinos were recruited by the United States Army. Twenty-six of the 30 American generals who served in the Philippines from 1898 to 1902 had fought in the Indian Wars.

By the end of February, 1899, the Americans had prevailed in the struggle for Manila, and the Philippine Army was forced to retreat north. Hard-fought American victories followed at Quingua (April), Zapote Bridge (June), and Tirad Pass (December). With the June assassination of General Antonio Luna by rivals in the Philippine leadership, conventional military leadership was weakened. Filipino Brigadier General Gregorio del Pilar fought a heroic delaying action at Battle of Tirad Pass to allow Aguinaldo to escape but del Pilar was killed in the final attack. For the Filipinos, this battle remains their Thermopylae. After this battle and the loss of two of their best generals, the Filipinos' ability to fight a conventional war rapidly diminished.