In the meantime, on January 23, 1899, the Malolos Constitution establishing the First Philippine Republic had been proclaimed and, on February 4, 1899, fighting had erupted in Manila between American and Filipino forces in what developed into the Philippine–American War.

[e] Aguinaldo was captured by the American forces on March 23, 1901, in Palanan, Isabela, he declared allegiance to the U.S. on April 19, 1901, effectively ending the Philippine Republic.

Aguinaldo himself had led a number of governments prior to Malolos, like those established at Tejeros and Biak-na-Bato which both styled themselves República de Filipinas ("Republic of the Philippines").

Unlike the founding documents of those governments, however, the Malolos Constitution was duly approved by a partially elected congress and called for a true representative democracy.

[20] The American naval commander, lacking forces to conduct land operations following his unexpectedly complete victory, returned Aguinaldo and a number of other revolutionary exiles to the Philippines from Hong Kong.

[26] The constitution written by the Malolos Congress was proclaimed on January 22, 1899, creating what is known today as the First Philippine Republic, with Aguinaldo as its president.

[34] That day President Aguinaldo issued a proclamation ordering and commanding that "peace and friendly relations with the Americans be broken and that the latter be treated as enemies, within the limits prescribed by the laws of war".

[37] On March 29, as American forces threatened Malolos, the seat of government moved to San Isidro, Nueva Ecija.

[42] Aguinaldo's party had already left Tarlac, the last capital of the Philippine Republic, by the time American troops occupied it on November 13.

[44] In October 1899, American forces were in San Fernando, Pampanga and the Philippine Republic was headquartered not far north of there, in Angeles City.

On October 12, an American offensive to the north forced the Philippine Republic to relocate its headquarters in November to Tarlac, and then to Bayambang, Pangasinan.

From that point on, distance and the localistic nature of the fighting prevented him from exercising a strong influence on revolutionary or military operations.

[43] Recognizing that American troops blocked his escape east, he turned north and west on November 15, crossing the mountains into La Union province.

After being notified by a rider of the outcome of the battle and the death of del Pilar, Aguinaldo ordered that camp be broken, and departed with his party for Cayan settlement.

Aguinaldo, encamped with his party about 10 km south of the pass in Cervantes, Ilocos Sur, was apprised of the result of the battle by a rider, and moved on.

[53] On August 27, 1900, after American forces landed at Aparri, Cagayan, Aguinaldo concluded that Tierra Virgan had become untenable as a headquarters and decided to march to Palanan, Isabela.

[62] Article 82 of the Malolos Constitution covered the organization and attributes of provincial and popular assemblies, and specified the principles governing local laws.

[63] Provisional Law on the Judiciary was issued on March 7, 1899, in accordance to the provisions of the 1899 Malolos Constitution providing that the Chief Justice shall be chosen by the National Assembly with the concurrence of the president and secretaries of the government.

[64][65][66] The Supreme Court included Gracio Gonzaga serving as president; Juan Arceo and Felix Ferrer as Chamber Presidents; and Deogracias Reyes, Juan Tongco, Pablo Tecson, and Ygnacio Villamor serving as Associate Justices[67] One of the important laws passed by the Malolos Congress was the law providing for a national loan to buoy up the national budget in which the Republic was trying to balance.

Aguinaldo then appointed Antonio Luna as Director or Assistant Secretary of War by September 28, 1898, and the Philippines first military school, the Academia Militar was established in Malolos.