From February 1856 a new Constitutional Congress convened, ending the next February, in which the radicals won out. The Ley Lerdo and Ley Juárez were ratified under the Constitution of 1857, which also saw to the protection of individual guarantees with the law of amparo (legal protection), as well as establishing freedom of education, of work, thought, the press, and the right to hold meetings. The new code, which instituted that the republic should be representative, democratic, and federal, established a new national project that sought a balance between the center and the states. It also confirmed the hegemony of the civil power and abolished the military and ecclesiastical privileges that had unleashed the Revolt of Zacapoaxtla. The division between Liberals and Conservatives was made very clear from the Constitution of 1857. The Conservatives stood by the church. The uprisings against the Constitution divided the Liberals: the diehards wanted to maintain it while the moderates sought further reforms or ignored it completely. Comonfort was undecided. As constitutional president-elect he took power on December 1, 1857, and had to govern with extraordinary powers while various constitutional articles on guarantees were suspended. The revolt grew and various conspiracies materialized.
On December 17, the Conservatives' Plan of Tacubaya was declared, which refused to recognize the Constitution but respected Comonfort. Various radicals were imprisoned, among them Juárez, president of the Supreme Court. Comonfort kept to the Plan, but in January 1858 Félix Zuloaga launched his coup d'état. The new revolt against Comonfort drove him into the arms of the Liberals, but a little later he handed over power to Juárez, next in line for the presidency under the Constitution of 1857. Juárez went to Guanajuato, setting up a government on January 19. Three days later a council in Mexico City nominated Zuloaga president of the country. The Liberal government counted on the support of 9 states, while 11 backed the Plan of Tacubaya.
Thus began the War of Reform, which would last three years and drive the church to revolt against the constitutional state. The war polarized society and radicalized positions. There were three stages: that of 1858, when the Conservatives had military successes; 1859, when forces were balanced; and 1860, when the Liberals recuperated and won. Juárez left Guanajuato for Guadalajara, but on the point of being arrested he fled to the Pacific coast and then to Veracruz, where he set up a government. On July 7, 1859, he expedited a manifesto proclaiming the separation of church and state, the suppression of monasteries, the confiscation of church goods, and the abolition of parish rights. All these elements were covered by various laws, jointly known as the Laws of the Reform.
