The Mexican reform movement was inspired by the liberal political philosophies of European intellectuals, such as Jean-Jacques Rousseau, John Stuart Mill, and Pierre Joseph Proudhon. Their views were adopted by a group of Mexican intellectuals who shared a strong commitment to moralize Mexican politics. The most outstanding member of the group was Benito Juárez, a Zapotec lawyer and politician. Juárez and his cohorts went into exile in Louisiana, where they drew up the Plan of Ayutla in 1854 for the overthrow of Santa Anna. As the plan gained broad-based support, the conspirators began to return to Mexico. In August 1855, in response to growing opposition, Santa Anna resigned for the last time.

A provisional government was installed under Juan Ruiz de Álvarez and the intellectuals of Ayutla; the ensuing period of liberal rule came to be known as the Reform. The Reform was touted as a Mexican version of the French Revolution. Several laws, known collectively as the Reform Laws, abolished the fueros , curtailed ecclesiastical property holdings, introduced a civil registry, and prohibited the church from charging exorbitant fees for administering the sacraments.

The Reform Laws polarized Mexican society along pro- and anticlerical lines at a time when delegates were preparing the constitution of 1857, as provided for in the Plan of Ayutla. The new constitution was derived from that of 1824, but it reflected a more liberal vision of society through its incorporation of the Reform Laws. It reaffirmed the abolition of slavery, secularized education, and guaranteed basic civil liberties for all Mexicans. Both the Reform Laws and the constitution, however, divided the political classes and set the stage for a civil war...

The civil war, commonly known as the War of the Reform, that engulfed Mexico between 1858 and 1861 brought to light the underlying conflicts that had been present in Mexican society since independence. The conservative faction launched the Plan of Tacubaya and, with the support of the military and the clergy, dissolved congress and arrested Juárez. Juárez escaped and established a "government in exile" in Querétaro (the liberals later moved their capital to Veracruz). The initial military advantage was held by the conservatives, who were better armed and had plentiful supplies, but by 1860 the situation was reversed. The final battle took place just before Christmas 1860. The victorious liberal army entered Mexico City on January 1, 1861.

In March 1861, Juárez won the presidential election, but the war left the treasury depleted. Trade was stagnant, and foreign creditors were demanding full repayment of Mexican debts. Juárez proceeded to declare a moratorium on all foreign debt repayments. In October 1861, Spain, Britain, and France decided to launch a joint occupation of the Mexican Gulf coast to force repayment. In December troops from the three nations landed at Veracruz and began deliberations. Because the representatives of the three nations could not agree on the means to enforce the collection of the debt, Britain and Spain recalled their armies. Spurred by dreams of reestablishing an empire in the New World, the French remained and, with the support of Mexican conservatives, embarked on an occupation of Mexico.

In Puebla, the French troops encountered strong resistance led by one of Juárez's trusted men, General Ignacio Zaragoza, who defeated the foreigners on May 5, 1862 (May 5 is celebrated today as one of Mexico's two national holidays). The following May, Puebla was surrounded once again by French troops, who laid siege to the city for two months until it surrendered. The fall of Puebla meant easy access to Mexico City, and Juárez decided to evacuate the capital after receiving approval from congress.

The French encountered no resistance to their occupation of Mexico City. In June 1863, a provisional government was chosen, and in October a delegation of Mexican conservatives invited Ferdinand Maximilian Joseph von Habsburg of Austria to accept the Mexican crown, all according to the plans of French emperor Napoleon III. Maximilian was a well-intentioned monarch who accepted the crown believing that this act responded to the desire of a majority of Mexicans. Before departing for Mexico, Maximilian signed an agreement with Napoleon III, under which Maximilian assumed the debts incurred for the upkeep of the French army in Mexico. On June 12, 1864, the Emperor Maximilian I and his Belgian wife, Marie Charlotte Amélie Léopoldine, now called Empress Carlota, arrived in Mexico City. The republican government under Juárez retreated to the far north.

Maximilian, schooled in the European liberal tradition, was a strong supporter of Mexican nationalism. He soon found resistance from all quarters of the political spectrum, however. The conservatives expected the emperor to act against the Reform Laws, but Maximilian refused to revoke them. Mexican liberals appealed for military assistance from the United States on the basis of the French violation of the 1823 Monroe Doctrine, but the United States was involved in its own civil war. The end of the Civil War in the United States in 1865, however, prompted a more assertive foreign policy toward Mexico and released manpower and arms that were directed to help Juárez in his fight against the French. In Europe, France was increasingly threatened by a belligerent Prussia. By November 1866, Napoleon III began recalling his troops stationed in Mexico. Conservative forces switched sides and began supporting the Mexican liberals. United republican forces resumed their campaign on February 19, 1867, and on May 15, Maximilian surrendered. He was tried and, on Juárez's orders, was executed on June 19.