The history of the Catholic Church in Mexico dates from the period of the Spanish conquest (1519–21) and has continued as an institution in Mexico into the twenty-first century. Catholicism is one of many major legacies from the Spanish colonial era, the others include Spanish as the nation's language, the Civil Code and Spanish colonial architecture. The Catholic Church was a privileged institution until the mid nineteenth century. It was the sole permissible church in the colonial era and into the early Mexican Republic, following independence in 1821. Following independence, it involved itself directly in politics, including in matters that did not specifically involve the Church.Anne Staples, "Clerics as Politicians: Church, State, and Political Power in Independent Mexico" in Mexico in the Age of Democratic Revolutions, 1750-1850. Jaime Rodríguez O., ed. Boulder: Lynne Rienner 1994.

In the mid-nineteenth century the liberal Reform brought major changes in church-state relations. Mexican liberals in power challenged the Catholic Church's role, particularly in reaction to its involvement in politics.Roderic Ai Camp, Crossing Swords: Politics and Religion in Mexico. Oxford University Press 1997, p. 25. The Reform curtailed the Church's role in education, property ownership, and control of birth, marriage, and death records, with specific anticlerical laws. Many of these were incorporated into the Constitution of 1857, restricting the Church's corporate ownership of property and other limitations. Although there were some liberal clerics who advocated reform, such as José María Luis Mora, the Church came to be seen as conservative and anti-revolutionary. During the bloody War of the Reform, the Church was an ally of conservative forces that attempted to oust the liberal government. They also were associated with the conservatives' attempt to regain power during the Second French intervention in Mexico, when Maximilian of Habsburg was invited to become emperor of Mexico. The empire fell and conservatives were discredited, along with the Catholic Church. However, during the long presidency of Porfirio Díaz (1876–1911) the liberal general pursued a policy of conciliation with the Catholic Church; though he kept the anticlerical articles of the liberal constitution in force, he in practice allowed greater freedom of action for the Catholic Church.Karl Schmitt, "The Díaz Policy on State and Local Levels, 1876–1911." Hispanic American Historical Review vol. 40, No. 4 (November 1960), pp. 513-532. With Díaz's ouster in 1911 and the decade-long conflict of the Mexican Revolution, the victorious Constitutionalist faction led by Venustiano Carranza wrote the new Constitution of 1917 that strengthened the anticlerical measures in the liberal Constitution of 1857.

With the presidency of Northern, anticlerical, revolutionary general Plutarco Elías Calles (1924–28), the State's enforcement of the anticlerical articles of Constitution of 1917 provoked a major crisis with violence in a number of regions of Mexico. The Cristero War (1926–29) was resolved, with the aid of diplomacy of the U.S. Ambassador to Mexico, ending the violence, but the anticlerical articles of the constitution remained. President Manuel Ávila Camacho (1940–1946) came to office declaring "I am a [Catholic] believer," (soy creyente) and Church-State relations improved though without constitutional changes.

A major change came in 1992, with the presidency of Carlos Salinas de Gortari (1988–1994). In a sweeping program of reform to "modernize Mexico" that he outlined in his 1988 inaugural address, his government pushed through revisions in the Mexican Constitution, explicitly including a new legal framework that restored the Catholic Church's juridical personality.Roberto Blancarte, "Recent Changes in Church-State Relations in Mexico: An Historical Approach." Journal of Church & State, Autumn 1993, Vol. 35, Issue 4.Jorge A. Vargas, "Freedom of Religion and Public Worship in Mexico: A Legal Commentary on the 1992 Federal Act on Religious Matters." BYU Law Review Vol. 1998, issue 2, article 6, pp. 421-481.Jorge A. Vargas, "Mexico's Legal Revolution: An Appraisal of Its Recent Constitutional Changes, 1988–1995." 25 Georgia Journal of International and Comparative Law, 497-559 (1996).Ricardo Hernández-Forcada, "The Effect of International Treaties on Religious Freedom in Mexico". 2002 BYU L. Rev. 301(202).Victor Gabriel Muro, "Catholic Church: Mexico" in Encyclopedia of Mexico vol. 1, p. 222. Chicago: Fitzroy Dearborn 1997. The majority of Mexicans in the twenty-first century identify themselves as being Catholic, but the growth of other religious groups such as Protestant evangelicals, Mormons, as well as secularism is consistent with trends elsewhere in Latin America. The 1992 federal Act on Religious Associations and Public Worship (Ley de Asociaciones Religiosas y Culto Público), known in English as the Religious Associations Act or (RAA), has affected all religious groups in Mexico.Vargas, "Freedom of religion and Public Worship in Mexico." The text of the act appears in English in the appendix of this article.

Colonial era (1521–1821)

Early period: The Spiritual Conquest 1519–1572

During the conquest, the Spaniards pursued a dual policy of military conquest, bringing indigenous peoples and territory under Spanish control, and spiritual conquest, that is, conversion of indigenous peoples to Christianity. When Spaniards embarked on the exploration and conquest of Mexico, a Catholic priest, Gerónimo de Aguilar, accompanied Hernán Cortés's expedition. Spaniards were appalled at the ritual practice of human sacrifice and initially attempted to suppress it, but until the Spanish conquest of the Aztec Empire was accomplished, it was not stamped out. The rulers of Cortés's allies from the city-state of Tlaxcala converted to Christianity almost immediately and there is a depiction of Cortés, Malinche, and the lords of Tlaxcala showing this event. But not until the fall of the Aztec capital of Tenochtitlan in 1521 was a full-scale conversion of the indigenous populations undertaken.

Power of the Spanish Crown in ecclesiastical matters

The justification of Spanish (and Portuguese) overseas conquests was to convert the existing populations to Christianity. The pope granted the Spanish monarch (and the crown of Portugal) broad concessions termed the Patronato Real or Royal Patronage, giving the monarch the power to appoint candidates for high ecclesiastical posts, collection of tithes and support of the clergy, but did not cede power in matters of doctrine or dogma.Ida Altman, Sarah Cline, and Javier Pescador, The Early History of Greater Mexico, Pearson 2003, 36. This essentially made the Spanish monarch the highest power of Church and State in its overseas territories.

The first evangelists to the indigenous

In the early conquest era of Mexico, the formal institutions of Church and State had not been established. But to initiate the spiritual conquest even though the episcopal hierarchy (the diocesan clergy) had not yet been established, Cortés requested that the mendicant orders of Franciscans, Dominicans, and Augustinians be sent to New Spain, to convert the indigenous. The Twelve Apostles of Mexico as they are known were the first Franciscans who arrived in 1524, followed by the Dominican order in 1526, and the Augustinian order in 1533.Altman, et al. Early History of Greater Mexico, p. 124.

Mendicants did not usually function as parish priests, administering the sacraments, but mendicants in early Mexico were given special dispensation to fulfill this function. The Franciscans, the first-arriving mendicants, staked out the densest and most central communities as their bases for conversion. These bases (called doctrina) saw the establishment of resident friars and the building of churches, often on the same sacred ground as pagan temples.

Given the small number of mendicants and the vast number of indigenous to convert, outlying populations of indigenous communities did not have resident priests but priests visited at intervals to perform the sacraments (mainly baptism, confession, and matrimony). In prehispanic Central Mexico, there had been a long tradition of conquered city-states adding the gods of their conquerors to their existing pantheon so that conversion to Christianity seemed to be similar.https://www.thebritishacademy.ac.uk/pubs/proc/files/81p163.pdf, p. 13

In Texcoco, however, a member of the native nobility, Don Carlos, was accused and convicted of sedition by the apostolic inquisition (which gives inquisitorial powers to a bishop) headed by Juan de Zumárraga in 1536 and was executed. His execution prompted the crown to reprimand Zumárraga and when the Holy Office of the Inquisition was established in Mexico in 1571, Indians were exempted from its jurisdiction. There was a concern that Indians were insufficiently indoctrinated in Catholic orthodox beliefs to be held to the same standards as Spaniards and other members of the República de Españoles. In the eyes of the Church and in Spanish law, Indians were legal minors.

Despite the fall of the Aztec Empire in 1521 at the hand of Hernán Cortés, it is arguable that Catholic conversion of the Indigenous peoples of Mexico didn’t truly begin until the arrival of the Twelve Apostles, a group of twelve Franciscan friars, in 1524. It has long been believed that the Indigenous of Mexico were passive in the conversion, with the majority simply accepting the new religion, thanks in part to the claims of the friars that the people were eager and devout converts from the beginning, though by the 1990s, historians began to wonder if that were really the case. Two concerns arise when considering how receptive the indigenous were to Catholicism. One crucial example being the Devil, for which there was no such person in Aztec belief, meaning there was already a huge disconnect when it came to vital understandings of Catholicism and the way in which it functions. Fray Toribio de Benavente Motolinia himself, wrote "And with this, each of the friars would speak as much and as best as they could about what would be best for the salvation of the Indians, but to them, it was a grand annoyance hearing the word of God and they did not want to understand anything but giving themselves to vices and sins ..." which implies that there was some difficulty in translation due to the fact that the Indigenous supposedly couldn’t understand anything the friars were teaching, and that some Indigenous didn’t care or got frustrated with the preaching of the friars thanks to the description of them being annoying, giving us a clearer image of how the Nahua truly felt about this new religion. The second would be that some Indigenous people of Mexico who welcomed this new god brought by the Spanish, did not exclusively believe in him, particularly those who were older, instead opting to add Jesus to their Pantheon, which led to the friars opting to focus on the more malleable younger generation.